DIVERSIDAD GENÉTICA/ESTADISITICA Y REDES DE CO-OCURRENCIA¶
Este tutorial utiliza un conjunto de datos de metabarcodificación reducido obtenido por C. Ribeiro y A. Lopes dos Santos. Este conjunto de datos se corresponde a la región 18S V4 amplificada en muestras clasificadas por citometría de flujo y secuenciada en una corrida Illumina 2*250 bp analizada con mothur.
Las simbiosis entre algas eucariotas y cianobacterias fijadoras de nitrógeno han sido reconocidas en los últimos años como una fuente clave de nuevo nitrógeno en los océanos. Se investigo la composición de las pequeñas comunidades de eucariotas fotosintéticos asociados con cianobacterias fijadoras de nitrógeno en la bahía del Atlántico Sur de Brasil utilizando una combinación de citometría de flujo y secuenciación de alto rendimiento de dos genes: la región V4 de 18S rRNA y nifH. Se encontraron dos comunidades eucariotas distintas, una dominada por las mamielofíceas " Bathycoccus y Ostreococcus ", y otra dominada por una primnesiófita conocida por vivir en simbiosis con la cianobacteria fijadora de nitrógeno UCYN-A1. Entre las secuencias nifH, las de UCYN-A1 fueron las más abundantes, pero también se encontraron otros tres clados UCYN-A (A2, A3, A4). El análisis de redes confirmó la relación entre los clados A1 y A2 y sus hospedadores hipotéticos y señaló la posible asociación entre el nuevo clado A4 y Braarudosphaera bigelowii, que anteriormente se había considerado hospedador de A2.
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# Paquetes necesarios (Descomentar para instalar)
# Generamos 3 objetos con la lista de paquetes provenientes de los repositorios CRAN, Bioconductor, y GitHub
# cran_packages <- c("factoextra", conflicted", "readxl", "knitr", "qtl", "bookdown", "magrittr", "plyr", "ggplot2", "grid", "gridExtra", "tidyverse", "devtools", "dplyr", "pheatmap", "xtable", "kableExtra", "remotes", "Rtsne", "vegan", "RColorBrewer", "PoiClaClu", "gtools")
# bioc_packages <- c("airway", "phyloseq", "dada2", "DECIPHER", "phangorn", "ggpubr","DESeq2", "genefilter", "philr", "GenomeInfoDb", "microbiome")
# git_source <- c("zdk123/SpiecEasi", "twbattaglia/btools", "gmteunisse/Fantaxtic", "MadsAlbertsen/ampvis2", "opisthokonta/tsnemicrobiota")
# git_packages <- c("btools", "fantaxtic", "ampvis2", "tsnemicrobiota")
# Instalar paquetes
# Las instrucciones a continuación, primero búscan aquellos paquetes que no han sido instalados
# y los guarda en el objeto (".inst""; el punto al inicio indica que es un objeto oculto)
# para luego instalar estos paquetes según el repositorio fuente
## Instalar paquetes CRAN
#.inst <- cran_packages %in% installed.packages()
#if(any(!.inst)) {
# install.packages(cran_packages[!.inst])
#}
## Instalar paquetes Bioconductor
### cargar la última versión de Bioconductor e instalar sus paquetes básicos
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#BiocManager::install()
### instalar paquetes
#.inst <- bioc_packages %in% installed.packages()
#if(any(!.inst)) {
# BiocManager::install(bioc_packages[!.inst])
#}
## Instalar paquetes GitHub
#.inst <- git_source %in% installed.packages()
#if(any(!.inst)) {
# devtools::install_github(git_source[!.inst])
#}
# Cargar paquetes en la actual sesión de R
#sapply(c(cran_packages, bioc_packages, git_packages), require, character.only = TRUE)
Phyloseq es un paquete de Bioconductor (Open Source Software For Bioinformatics) para la manipulación y análisis de datos metagenómicos generados por metodologías de secuenciación de alto rendimiento. Phyloseq es una herramienta para importar, guardar, analizar y visualizar éste tipo de datos después de haber sido procesados inicialmente, e.g., ensamblaje de novo, ASVs u OTUs (clustered), incluyendo otros importantes datos asociados (si están disponibles): tabla de observaciones asociadas a cada muestra (e.g., especie, localización geográfica, temperatura, etc.), conocida como sample data o metadata, árbol filogenético, e identificación taxonómica de cada OTU. La estructura del paquete phyloseq consiste en una serie de funciones de acceso y de proceso de objetos phyloseq. Estos objetos están compuestos de cuatro componentes que almacenan las cuentas de reads, la metadata, la taxonomía y el árbol filogenético. El paquete también provee una serie de herramientas para importar datos de otros programas. El siguiente diagrama muestra la estructura completa de phyloseq
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# libreria
library("conflicted")
library("knitr")
library("qtl")
library("bookdown")
library("magrittr")
library("plyr")
library("ggplot2") # esencial
library("grid")
library("gridExtra")
library("tidyverse")
library("devtools")
library("dplyr") # esencial
library("pheatmap")
library("xtable")
library("kableExtra")
library("remotes")
library("Rtsne")
library("vegan")
library("RColorBrewer")
library("PoiClaClu")
library("gtools")
library("airway")
library("phyloseq") # esencial
library("dada2")
library("DECIPHER")
library("phangorn")
library("ggpubr")
library("DESeq2")
library("genefilter")
library("philr")
library("GenomeInfoDb")
library("microbiome")
library("btools")
library("tsnemicrobiota")
library("fantaxtic")
library("ampvis2")
library("tsnemicrobiota")
library("readxl") # esencial
library("SpiecEasi") # esencial
library("FactoMineR")
library("factoextra")
library("Matrix")
library("igraph")
Cambie tu directorio de trabajo al lugar donde se encuentran los archivos
Se necesitan tres tablas
OTU Taxonomía Muestras Se leen de un único archivo Excel en el que cada hoja contiene una de las tablas
CONCEPTOS¶
En los análisis filogenéticos, una unidad taxonómica operativa (UTO), también conocida por la sigla OTU. Operational Taxonomic Unit—es una unidad de clasificación seleccionada por el investigador que la utiliza para individualizar a objetos de su estudio, ya sea una especie u otro taxón de cualquier categoría,una morfoespecie, una población, y hasta un individuo, y de este modo poder ordenarlos en una clasificación y en la construcción de un árbol filogenético, sin juzgar si se corresponden a una entidad biológica particular
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otu_mat<- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "OTU matrix")
print(otu_mat)
tax_mat<- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "Taxonomy table")
print(tax_mat)
samples_df <- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "Samples")
print(samples_df)
# A tibble: 287 x 56 otu X10n X10p X11n X11p X120n X120p X121n X121p X122n X122p X125n X125p <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> 1 Otu0~ 13679 6292 42 2500 18850 5 43 7138 9432 10541 9 9772 2 Otu0~ 18 7134 38 9830 45 61420 182 23751 36 11 4535 3502 3 Otu0~ 9939 8983 31 13 24620 19 19 16 12502 3831 4621 2240 4 Otu0~ 3675 4234 24 22 11 16 32967 35 6 18 6908 5 5 Otu0~ 0 5 0 7 0 8 0 16 20166 0 0 2 6 Otu0~ 0 8 0 0 0 8 0 0 5 3 3 0 7 Otu0~ 4587 518 4 386 8775 5 6 1102 14336 0 0 3626 8 Otu0~ 1 8 2 4408 3 29 6 12355 0 0 0 0 9 Otu0~ 115 914 3 325 0 629 1 834 5 0 1354 2108 10 Otu0~ 780 8 23810 12 3279 0 12 7 3027 0 2 4156 # i 277 more rows # i 43 more variables: X126n <dbl>, X126p <dbl>, X127n <dbl>, X13n <dbl>, # X13p <dbl>, X140n <dbl>, X140p <dbl>, X141n <dbl>, X141p <dbl>, # X142n <dbl>, X142p <dbl>, X155n <dbl>, X155p <dbl>, X156n <dbl>, # X156p <dbl>, X157n <dbl>, X157p <dbl>, X15n <dbl>, X15p <dbl>, X165n <dbl>, # X165p <dbl>, X166n <dbl>, X166p <dbl>, X167n <dbl>, X167p <dbl>, X1n <dbl>, # X1p <dbl>, X2n <dbl>, X2p <dbl>, X3n <dbl>, X3p <dbl>, X5n <dbl>, ...
# A tibble: 287 x 8 otu Domain Supergroup Division Class Order Family Genus <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> 1 Otu001 Eukaryota Archaeplastida Chlorophyta Mamiellophyce~ Mami~ Bathy~ Ostr~ 2 Otu002 Eukaryota Hacrobia Haptophyta Prymnesiophyc~ Prym~ Braar~ UCYN~ 3 Otu003 Eukaryota Archaeplastida Chlorophyta Mamiellophyce~ Mami~ Bathy~ Bath~ 4 Otu004 Eukaryota Alveolata Dinophyta Dinophyceae Dino~ Dinop~ Pror~ 5 Otu005 Eukaryota Stramenopiles Ochrophyta Bacillariophy~ Medi~ Medio~ Thal~ 6 Otu006 Eukaryota Stramenopiles Ochrophyta Bacillariophy~ Baci~ Bacil~ Pseu~ 7 Otu007 Eukaryota Stramenopiles Ochrophyta Pelagophyceae Pela~ Pelag~ Pela~ 8 Otu008 Eukaryota Alveolata Dinophyta Dinophyceae Dino~ Dinop~ Dino~ 9 Otu009 Eukaryota Hacrobia Haptophyta Prymnesiophyc~ Prym~ Chrys~ Chry~ 10 Otu010 Eukaryota Opisthokonta Metazoa Craniata Cran~ Crani~ Cran~ # i 277 more rows # A tibble: 55 x 29 sample fraction Select_18S_nifH total_18S total_16S total_nifH sample_number <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr> 1 X10n Nano Yes 53230 8772 36 10 2 X10p Pico Yes 47390 4448 6241 10 3 X11n Nano No 24007 6193 3772 11 4 X11p Pico Yes 31899 14 10201 11 5 X120n Nano Yes 70455 5292 93 120 6 X120p Pico Yes 76182 53272 23147 120 7 X121n Nano Yes 52401 5958 26838 121 8 X121p Pico Yes 71785 10993 23706 121 9 X122n Nano Yes 78740 11730 15543 122 10 X122p Pico Yes 37364 11817 11045 122 # i 45 more rows # i 22 more variables: transect <dbl>, station <chr>, depth <dbl>, # latitude <dbl>, longitude <dbl>, picoeuks <dbl>, nanoeuks <dbl>, # bottom_depth <dbl>, level <chr>, transect_distance <dbl>, date <chr>, # time <chr>, phosphates <chr>, silicates <chr>, ammonia <chr>, # nitrates <chr>, nitrites <chr>, temperature <chr>, fluorescence <chr>, # salinity <chr>, sample_label <chr>, costa <chr>
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# Los objetos Phyloseq deben tener nombres de fila.
# definir los nombres de las filas de la columna otu
# tibble es una versión mejorada de la clase de objeto "data.frame".
# *Los nombres de las variables se preservar tal como se ingresaron
# *Los tibbles tienen un formato más limpio y fácil de leer que los data.frames
# *Las variables se imprimen en columnas separadas, lo que facilita la visualización de los datos
otu_mat <- otu_mat %>%
tibble::column_to_rownames("otu")
print(otu_mat)
X10n X10p X11n X11p X120n X120p X121n X121p X122n X122p X125n X125p
Otu001 13679 6292 42 2500 18850 5 43 7138 9432 10541 9 9772
Otu002 18 7134 38 9830 45 61420 182 23751 36 11 4535 3502
Otu003 9939 8983 31 13 24620 19 19 16 12502 3831 4621 2240
Otu004 3675 4234 24 22 11 16 32967 35 6 18 6908 5
Otu005 0 5 0 7 0 8 0 16 20166 0 0 2
Otu006 0 8 0 0 0 8 0 0 5 3 3 0
Otu007 4587 518 4 386 8775 5 6 1102 14336 0 0 3626
Otu008 1 8 2 4408 3 29 6 12355 0 0 0 0
Otu009 115 914 3 325 0 629 1 834 5 0 1354 2108
Otu010 780 8 23810 12 3279 0 12 7 3027 0 2 4156
Otu011 0 3 2 2 0 13 5 5 4 7 3081 11
Otu012 0 0 0 6 0 0 0 16 3 0 0 0
Otu013 6321 2471 2 0 12 3 0 0 4 20272 0 15
Otu014 0 82 4 3304 1 1667 4 9233 13 3 0 2707
Otu015 0 12 0 3 7 25 1 6 10 0 4 2772
Otu016 1 0 0 9 5 0 0 14 0 0 0 0
Otu017 0 0 0 0 0 0 0 0 17 8 0 0
Otu018 1 0 9 911 0 0 15 2702 6 4 342 2217
Otu019 0 0 13 0 0 0 29 0 0 0 0 0
Otu020 425 0 1 0 1706 0 8447 1 0 0 0 0
Otu021 0 4 0 0 0 10 0 0 0 0 2 0
Otu022 0 0 0 4987 0 0 0 6 90 1 1 524
Otu023 4 0 1 0 0 3 0 0 0 0 0 0
Otu024 0 0 0 0 0 0 0 0 0 0 0 17
Otu025 69 0 0 0 290 0 0 0 21 0 118 2
Otu026 0 2 0 0 0 3 0 0 0 1 0 0
Otu027 6 2304 0 0 5 0 0 0 57 4 0 14529
Otu028 19 467 0 363 79 0 1 816 1 0 190 0
Otu029 0 1271 0 1 0 0 1794 1 1762 929 923 0
Otu030 0 5 0 0 0 4 0 0 155 0 1 0
Otu031 5 3945 0 0 0 0 0 7 2297 0 0 0
Otu032 0 8 10 0 0 16 19 5 0 3 0 4
Otu033 0 0 0 0 0 7 0 0 0 0 0 0
Otu034 0 0 0 0 0 0 0 0 0 0 3 0
Otu035 4 0 0 1 0 0 7 0 2 4 2499 1
Otu036 6 0 0 0 10 0 0 0 0 0 0 0
Otu037 0 0 0 5 0 0 0 7 0 0 0 0
Otu038 0 0 0 552 0 2 0 1518 3 0 0 0
Otu039 163 0 0 0 516 0 229 2 4 0 0 0
Otu040 1250 0 0 0 2 0 0 17 1660 0 0 0
Otu041 1 0 0 1 2 1 0 5 4 1 0 0
Otu042 3 0 0 0 7 0 0 0 0 0 0 0
Otu043 2818 0 0 0 8969 0 0 2 0 0 0 0
Otu044 1596 0 3 0 2 0 7 0 8 3 2 2484
Otu045 0 0 0 0 0 0 0 0 0 5 0 0
Otu046 0 1 0 0 0 0 0 0 0 0 0 0
Otu047 0 0 0 779 1 0 3 2460 0 1 0 0
Otu048 4 0 0 0 6 0 0 0 0 0 0 0
Otu049 0 0 0 2170 1 2 0 6430 3 0 0 1548
Otu050 2 0 0 0 4 0 0 0 0 0 0 0
Otu051 74 59 0 169 305 0 6 483 0 8 40 63
Otu052 3 0 0 0 4 0 0 0 0 0 0 0
Otu053 6651 0 0 0 3 0 0 0 0 0 0 0
Otu054 0 0 0 0 0 0 0 0 0 1 0 0
Otu055 0 0 0 0 0 2 0 0 0 0 0 0
Otu056 0 6374 1 3 0 7 0 0 0 0 1 0
Otu057 0 0 2 0 0 0 0 0 3 1123 812 596
Otu058 1 0 0 0 0 0 0 0 0 0 0 0
Otu059 0 0 0 2 0 1 0 9 0 1 0 3
Otu060 0 473 0 0 0 6699 0 0 0 0 0 0
Otu061 0 0 0 0 0 0 0 0 4 0 0 0
Otu062 0 0 0 0 0 2 0 1 0 0 0 0
Otu063 0 0 0 0 0 0 0 0 6382 0 0 5
Otu064 0 0 0 0 0 0 0 0 0 0 0 0
Otu065 164 0 0 0 729 0 0 1 0 0 0 0
Otu066 0 38 0 0 0 426 0 0 92 1 0 262
Otu067 0 0 0 0 0 0 0 0 1720 0 1 0
Otu068 0 0 1 0 0 0 1031 0 0 0 0 0
Otu069 0 0 0 0 0 0 0 3 1 0 0 0
Otu070 0 0 0 0 0 0 0 0 0 201 0 3
Otu071 0 0 0 0 0 1 0 0 0 0 0 0
Otu072 1 7 0 0 0 70 0 0 0 0 0 21
Otu073 0 0 0 0 0 0 0 0 0 0 0 0
Otu074 0 0 0 0 0 0 0 0 0 2 0 208
Otu075 0 0 0 1 4 0 0 0 4 0 0 1
Otu076 0 0 0 0 3 0 0 0 4 0 0 0
Otu077 0 1 0 0 0 0 0 0 0 0 0 0
Otu078 1 107 0 287 0 1254 1 759 0 0 0 0
Otu079 0 0 0 0 0 0 0 0 4154 0 0 0
Otu080 0 1 0 0 0 0 1 0 0 0 0 0
Otu081 0 0 0 0 0 0 0 0 0 0 0 0
Otu082 0 0 0 0 0 0 0 0 0 0 0 0
Otu083 0 0 0 1 0 0 0 2 0 0 0 0
Otu084 0 0 0 0 0 0 0 0 0 0 0 0
Otu085 263 7 0 0 1119 128 0 0 0 2 0 0
Otu086 0 0 0 0 0 0 1 0 0 0 0 0
Otu087 0 0 0 0 0 0 0 0 0 0 0 0
Otu088 0 244 0 0 0 2903 0 0 0 0 0 0
Otu089 0 0 1 0 0 0 0 0 0 0 0 0
Otu090 0 0 0 0 0 1 0 0 0 0 0 0
Otu091 0 0 0 0 0 0 0 0 0 0 0 0
Otu092 0 0 0 0 0 0 0 0 0 0 0 0
Otu093 0 0 0 1 0 0 0 1 0 0 0 0
Otu094 0 0 0 763 0 1 0 1820 0 0 0 0
Otu095 0 0 0 0 0 0 136 0 0 0 582 0
Otu096 0 0 0 0 0 0 2459 0 0 0 0 0
Otu097 0 0 0 0 0 0 0 0 1 0 0 0
Otu098 0 0 0 0 0 0 2 0 0 0 0 0
Otu099 0 0 0 0 0 0 2 0 0 0 0 0
Otu100 0 0 0 0 0 0 0 0 0 0 0 0
Otu101 0 0 0 0 0 0 0 0 0 0 0 0
Otu102 0 0 0 2 0 0 0 0 0 0 0 0
Otu103 0 34 0 0 0 236 0 0 0 0 0 59
Otu104 0 0 0 0 0 0 0 0 0 0 0 735
Otu105 0 0 0 0 0 0 0 0 0 0 0 0
Otu106 0 0 0 1 0 0 0 0 0 0 0 0
Otu107 0 0 1 0 0 0 0 0 0 0 0 0
Otu108 0 0 0 0 3 0 0 0 0 0 0 0
Otu109 0 0 0 0 0 0 0 0 0 0 0 0
Otu110 0 0 0 0 0 0 0 0 0 0 0 0
Otu111 0 0 0 0 0 0 0 0 0 0 0 0
Otu112 0 0 0 0 0 0 0 0 0 0 0 0
Otu113 0 0 0 0 0 0 1027 0 0 0 0 0
Otu114 88 38 1 0 104 0 0 0 36 35 0 51
Otu115 0 0 0 0 0 0 1530 0 0 0 0 0
Otu116 0 0 0 0 0 0 0 0 0 0 0 0
Otu117 0 0 0 0 0 0 0 2 0 0 0 0
Otu118 0 0 0 0 0 0 0 0 0 0 0 0
Otu119 0 0 0 0 0 0 0 0 0 0 8 0
Otu120 64 25 0 0 165 0 0 0 28 19 13 6
Otu121 0 0 0 1 0 0 0 0 0 0 0 0
Otu122 0 1109 0 0 0 2 0 0 0 0 0 0
Otu123 191 15 0 0 34 0 0 0 30 32 0 34
Otu124 0 0 0 0 0 0 0 0 0 0 0 0
Otu125 0 0 0 0 0 0 0 0 0 0 0 0
Otu126 0 0 0 0 0 0 0 0 0 0 0 0
Otu127 0 0 0 0 0 0 0 0 3 0 0 745
Otu128 0 0 0 0 0 0 0 0 0 0 0 0
Otu129 0 0 0 0 0 0 0 0 0 0 0 0
Otu130 0 0 0 0 0 0 887 0 0 0 0 0
Otu131 0 0 0 0 0 0 0 0 0 0 0 0
Otu132 0 0 0 0 0 0 0 0 1 0 209 1
Otu133 0 0 0 0 0 0 0 0 0 0 0 0
Otu134 0 0 0 0 0 0 0 0 0 0 0 0
Otu135 150 0 0 0 586 0 0 0 0 0 0 0
Otu136 0 0 0 0 0 1 732 0 0 0 0 0
Otu137 0 0 0 0 0 0 0 0 0 0 0 0
Otu138 0 0 0 0 0 0 0 0 424 0 0 49
Otu139 0 0 0 0 0 0 0 0 0 0 0 0
Otu140 0 0 0 0 0 0 0 0 0 0 0 0
Otu141 25 7 0 0 35 0 0 0 21 25 0 9
Otu142 0 0 0 0 0 0 0 0 0 0 0 0
Otu143 0 0 0 0 0 0 0 0 0 0 0 0
Otu144 0 0 0 0 0 0 0 0 0 0 0 0
Otu145 0 0 0 0 0 1 0 0 0 0 0 0
Otu146 0 0 0 0 0 0 0 0 0 0 264 0
Otu147 0 0 0 0 0 0 0 0 0 0 0 0
Otu148 0 48 0 0 0 520 0 0 0 0 0 0
Otu149 0 0 0 0 0 0 0 0 0 0 0 0
Otu150 0 0 0 0 0 0 0 0 0 0 0 0
Otu151 0 0 0 0 0 0 0 0 0 0 0 0
Otu152 0 0 1 0 0 0 0 0 2 0 458 0
Otu153 0 0 0 0 0 0 465 0 0 0 0 0
Otu154 0 0 0 0 0 0 0 0 0 0 0 0
Otu155 0 0 0 0 0 0 0 0 0 0 0 0
Otu156 16 15 0 0 34 0 0 0 16 6 8 0
Otu157 0 0 0 0 0 0 0 0 0 0 0 0
Otu158 0 0 0 0 0 0 0 0 0 0 0 0
Otu159 0 0 0 0 0 0 0 0 0 0 0 0
Otu160 0 0 0 0 0 0 0 0 0 0 0 0
Otu161 0 0 0 0 0 0 0 0 0 0 0 0
Otu162 0 0 0 0 0 0 323 0 0 0 0 0
Otu163 0 0 0 0 0 0 1 0 0 0 313 0
Otu164 0 1 0 0 0 0 0 0 0 0 0 0
Otu165 0 0 0 0 0 0 0 0 0 0 0 0
Otu166 0 0 0 0 0 0 0 0 1 0 0 0
Otu167 0 0 0 0 0 0 0 0 0 0 0 0
Otu168 1 0 0 0 0 0 0 0 0 0 0 0
Otu169 0 0 0 0 0 0 0 0 0 0 0 0
Otu170 0 0 0 0 0 0 0 0 0 0 0 0
Otu171 0 1 0 0 0 0 0 0 0 0 0 0
Otu172 0 0 0 0 0 0 0 0 0 0 0 0
Otu173 0 0 0 0 0 0 0 0 0 242 0 0
Otu174 0 0 0 25 0 7 0 42 0 0 0 13
Otu175 0 0 0 0 0 0 0 0 0 0 0 0
Otu176 0 1 0 0 0 0 0 0 0 0 0 0
Otu177 0 0 0 0 0 0 0 0 0 0 0 0
Otu178 0 0 0 0 0 0 0 0 0 0 0 0
Otu179 0 0 0 0 0 0 0 0 0 0 0 0
Otu180 0 0 0 0 0 0 0 0 0 0 0 0
Otu181 0 0 0 0 0 0 0 0 0 0 14 1
Otu182 3 17 0 0 5 0 0 0 29 3 9 0
Otu183 0 0 0 0 0 0 0 0 0 0 0 0
Otu184 0 0 0 0 0 0 0 0 0 0 0 0
Otu185 5 1 0 0 18 0 0 0 6 2 3 0
Otu186 0 0 0 0 0 0 0 0 0 0 0 0
Otu187 0 0 0 0 0 0 0 0 0 0 0 0
Otu188 7 5 0 0 16 0 0 0 4 2 3 0
Otu189 0 0 0 0 0 0 0 0 0 0 11 0
Otu190 0 0 0 0 0 0 0 0 0 0 0 0
Otu191 0 0 0 0 0 0 0 1 0 0 0 0
Otu192 0 0 0 0 0 0 0 0 0 0 0 0
Otu193 0 0 0 0 0 0 0 0 0 0 0 0
Otu194 0 0 0 0 0 0 0 0 0 0 0 0
Otu195 0 0 0 0 0 0 0 0 0 0 0 0
Otu196 0 0 0 0 0 0 0 0 118 0 0 0
Otu197 0 0 0 0 0 0 0 0 0 0 0 0
Otu198 0 0 0 0 0 0 0 0 0 0 0 0
Otu199 0 0 0 24 0 0 0 74 0 0 0 7
Otu200 0 0 0 0 0 0 0 0 0 0 0 0
Otu201 0 0 0 0 0 0 0 0 0 0 0 0
Otu202 0 0 0 0 0 0 0 0 0 0 0 0
Otu203 0 0 0 0 0 0 0 0 0 0 0 0
Otu204 0 0 0 0 0 0 0 0 0 0 0 0
Otu205 0 0 0 0 0 0 0 0 0 0 0 0
Otu206 0 0 0 0 0 0 0 0 0 0 12 0
Otu207 0 0 0 0 0 0 0 0 0 0 0 0
Otu208 0 0 0 0 0 0 0 0 0 0 0 0
Otu209 7 0 0 0 13 0 0 0 0 0 0 0
Otu210 3 3 0 0 5 0 0 0 4 3 0 1
Otu211 0 0 0 0 0 0 0 0 0 0 1 0
Otu212 0 0 0 0 0 0 0 0 0 0 0 0
Otu213 0 0 0 0 0 0 0 0 0 0 0 0
Otu214 0 0 0 0 0 0 0 0 0 0 0 0
Otu215 0 0 0 0 0 0 0 0 0 0 0 0
Otu216 0 0 0 0 0 0 0 0 0 0 0 0
Otu217 0 0 0 0 0 0 0 0 0 0 0 0
Otu218 0 0 0 12 0 0 0 33 0 0 0 0
Otu219 5 3 0 0 2 0 0 0 0 0 4 0
Otu220 0 0 0 0 0 0 0 0 0 0 0 0
Otu221 0 0 0 0 0 0 0 0 0 0 0 0
Otu222 4 3 0 0 0 0 0 0 2 0 0 1
Otu223 0 0 0 0 0 0 0 0 0 0 13 0
Otu224 0 0 0 0 0 0 0 0 0 0 0 0
Otu225 0 0 0 0 0 0 0 0 0 0 0 0
Otu226 0 0 0 0 0 0 0 0 0 0 0 0
Otu227 0 3 0 0 5 0 0 0 4 0 3 0
Otu228 0 2 0 0 1 0 0 0 0 0 0 3
Otu229 0 0 0 0 0 0 0 0 0 0 0 47
Otu230 2 0 0 0 2 0 0 0 2 1 0 0
Otu231 0 0 0 0 0 0 0 0 0 0 0 0
Otu232 0 0 0 0 0 0 0 0 0 0 0 0
Otu233 0 0 0 0 0 0 0 0 0 0 0 0
Otu234 0 1 0 0 4 0 0 0 2 0 0 0
Otu235 0 0 0 0 0 0 0 0 0 0 0 0
Otu236 0 0 0 3 0 0 0 14 0 0 0 0
Otu237 4 0 0 0 7 0 0 0 0 0 0 0
Otu238 0 0 0 0 0 0 0 0 0 4 0 0
Otu239 0 32 0 0 0 0 0 0 0 0 0 0
Otu240 0 32 0 0 0 0 0 0 0 0 0 0
Otu241 0 0 0 0 0 0 0 0 0 0 0 0
Otu242 0 2 0 0 3 0 0 0 0 0 0 0
Otu243 0 0 0 0 0 0 0 0 0 0 0 0
Otu244 0 0 0 0 0 0 0 0 0 0 0 0
Otu245 0 0 0 0 3 0 0 0 0 0 0 0
Otu246 0 0 0 0 0 0 0 0 0 0 0 0
Otu247 0 0 0 0 0 25 0 0 0 0 0 0
Otu248 0 0 0 0 0 0 0 0 0 0 0 0
Otu249 0 0 0 0 12 0 0 0 0 0 0 0
Otu250 0 0 0 0 0 0 0 0 0 0 0 0
Otu251 1 1 0 0 0 0 0 0 0 0 0 1
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Otu031 0 0 0 0 0 0
Otu032 0 0 0 8 7 3
Otu033 0 6 1 20397 3 4
Otu034 3 0 0 0 0 0
Otu035 2696 4 5 0 0 0
Otu036 0 0 7 0 0 0
Otu037 0 0 0 0 0 0
Otu038 2491 1 4 3 2 0
Otu039 0 0 0 0 0 0
Otu040 0 0 3 0 0 6
Otu041 3333 1 3 0 2 0
Otu042 0 1 2 0 0 0
Otu043 0 0 1 0 0 0
Otu044 0 3 3 0 2 0
Otu045 0 0 0 0 0 0
Otu046 0 0 0 1 0 0
Otu047 0 0 0 0 0 0
Otu048 0 0 6 0 0 0
Otu049 0 2 0 0 0 4
Otu050 0 0 2 0 1 0
Otu051 5 1 934 144 8 1
Otu052 1182 3 7868 2 1 1
Otu053 0 0 0 0 0 0
Otu054 0 6 2 2 3 3
Otu055 0 1 0 8684 0 0
Otu056 0 0 0 0 0 0
Otu057 1 0 0 0 1 0
Otu058 0 3 5 0 0 0
Otu059 0 0 0 0 0 0
Otu060 0 0 0 0 0 0
Otu061 0 0 0 0 0 0
Otu062 0 0 0 1 0 0
Otu063 0 0 0 0 0 0
Otu064 0 1 6 0 3 6
Otu065 0 1 0 0 0 0
Otu066 0 0 0 0 0 0
Otu067 0 0 0 0 0 0
Otu068 0 0 0 0 0 0
Otu069 0 0 0 0 0 0
Otu070 0 2 0 0 0 0
Otu071 0 0 0 2 0 0
Otu072 0 0 3787 279 0 1
Otu073 0 0 0 1 0 0
Otu074 2 0 0 0 0 0
Otu075 0 0 3 0 689 1
Otu076 0 0 0 0 0 0
Otu077 0 0 0 0 0 0
Otu078 0 0 0 0 0 1
Otu079 0 0 0 0 0 0
Otu080 0 0 0 0 0 0
Otu081 0 0 0 0 0 0
Otu082 0 1 0 0 0 0
Otu083 0 0 0 0 0 3
Otu084 0 0 0 0 0 0
Otu085 0 0 0 0 0 0
Otu086 0 0 0 0 2 0
Otu087 0 0 0 1 0 0
Otu088 0 0 0 1 0 0
Otu089 0 0 0 0 0 0
Otu090 0 0 0 3 0 0
Otu091 0 0 0 0 0 0
Otu092 0 0 0 0 2823 0
Otu093 0 0 0 0 0 0
Otu094 0 0 0 0 0 0
Otu095 0 0 0 0 0 2
Otu096 0 0 0 0 1 0
Otu097 0 0 0 0 0 0
Otu098 0 0 0 0 0 0
Otu099 0 0 0 0 1 0
Otu100 0 0 0 0 0 1
Otu101 0 0 0 0 0 0
Otu102 0 0 0 0 0 1846
Otu103 0 0 0 921 0 2
Otu104 0 0 0 0 0 0
Otu105 0 0 0 0 0 0
Otu106 0 0 0 0 0 1
Otu107 0 0 0 0 0 0
Otu108 0 0 0 0 0 0
Otu109 0 0 0 0 0 1
Otu110 0 0 0 0 1 0
Otu111 0 0 0 0 0 0
Otu112 0 0 0 0 0 0
Otu113 0 0 0 0 0 0
Otu114 0 0 1 0 0 0
Otu115 0 0 0 0 1 0
Otu116 0 0 0 0 0 0
Otu117 0 0 1 0 0 1491
Otu118 0 0 0 0 0 0
Otu119 2 0 0 0 0 0
Otu120 0 0 1 0 0 0
Otu121 0 0 0 0 0 1
Otu122 0 0 0 0 0 0
Otu123 0 0 1 0 0 0
Otu124 0 0 0 0 0 0
Otu125 0 0 0 0 0 0
Otu126 0 0 0 0 0 1
Otu127 0 0 0 0 0 0
Otu128 0 0 0 0 0 658
Otu129 0 0 0 0 0 0
Otu130 0 0 0 0 0 0
Otu131 0 0 0 0 0 0
Otu132 0 0 0 0 0 0
Otu133 0 1 0 0 0 0
Otu134 0 0 0 0 0 0
Otu135 0 0 0 0 0 0
Otu136 0 0 0 0 0 0
Otu137 0 0 0 0 0 0
Otu138 0 0 0 0 0 0
Otu139 0 0 0 0 0 0
Otu140 0 0 0 0 0 0
Otu141 0 0 0 0 0 0
Otu142 0 0 0 0 0 0
Otu143 0 0 0 0 0 1
Otu144 0 0 0 0 0 0
Otu145 0 0 0 0 0 0
Otu146 0 0 0 0 0 0
Otu147 0 0 0 0 0 0
Otu148 0 0 0 0 0 0
Otu149 0 1 0 0 0 0
Otu150 0 0 0 0 0 0
Otu151 0 0 0 0 0 0
Otu152 0 0 0 0 2 0
Otu153 0 0 0 0 0 0
Otu154 0 0 0 0 0 0
Otu155 0 0 0 0 0 0
Otu156 0 0 0 0 0 0
Otu157 0 0 0 0 0 0
Otu158 0 0 0 0 0 0
Otu159 0 0 0 0 0 0
Otu160 0 0 0 0 0 0
Otu161 0 0 0 0 0 258
Otu162 0 0 0 0 0 0
Otu163 0 0 0 0 0 0
Otu164 0 0 0 0 0 0
Otu165 0 0 0 0 0 0
Otu166 0 0 0 0 0 0
Otu167 0 0 0 0 0 0
Otu168 0 0 0 0 0 0
Otu169 0 0 0 0 0 229
Otu170 0 0 0 0 0 0
Otu171 0 0 0 0 0 0
Otu172 0 0 0 1 0 0
Otu173 0 0 0 0 0 0
Otu174 0 0 0 0 0 0
Otu175 0 0 0 0 0 0
Otu176 0 0 0 0 0 0
Otu177 0 0 0 0 0 0
Otu178 0 0 0 0 0 0
Otu179 0 0 0 0 0 0
Otu180 0 0 0 0 0 0
Otu181 0 0 0 0 0 0
Otu182 0 0 0 0 0 0
Otu183 0 0 0 0 0 0
Otu184 0 0 0 0 0 0
Otu185 0 0 0 0 0 0
Otu186 0 0 0 0 0 0
Otu187 0 0 0 0 0 107
Otu188 0 0 0 0 0 0
Otu189 0 0 0 0 0 0
Otu190 0 0 0 0 0 0
Otu191 0 0 0 0 0 0
Otu192 0 0 0 0 0 0
Otu193 0 0 0 0 0 0
Otu194 0 0 0 0 0 0
Otu195 0 0 124 0 0 0
Otu196 0 0 0 0 0 0
Otu197 0 0 0 0 0 0
Otu198 0 0 0 0 0 0
Otu199 0 0 0 0 0 0
Otu200 0 1 0 0 0 0
Otu201 0 0 0 0 0 0
Otu202 0 0 0 0 0 0
Otu203 95 1 0 0 1 0
Otu204 0 0 0 0 0 0
Otu205 0 0 0 0 0 0
Otu206 19 0 0 0 0 0
Otu207 0 0 0 0 0 0
Otu208 0 0 0 1 0 0
Otu209 0 0 0 0 0 0
Otu210 0 0 0 0 0 0
Otu211 0 0 0 0 22 0
Otu212 0 0 0 0 0 0
Otu213 0 0 0 0 0 0
Otu214 0 0 0 0 0 0
Otu215 0 0 0 0 0 0
Otu216 0 0 0 0 0 0
Otu217 15 0 1 0 0 0
Otu218 0 0 0 0 0 0
Otu219 0 0 0 0 0 0
Otu220 0 0 0 0 0 0
Otu221 0 0 0 0 0 0
Otu222 0 0 0 0 0 0
Otu223 0 0 0 0 0 0
Otu224 0 0 0 0 0 0
Otu225 0 0 0 0 0 0
Otu226 0 0 0 0 0 0
Otu227 0 0 0 0 0 0
Otu228 0 0 0 0 0 0
Otu229 0 0 0 0 0 0
Otu230 0 0 0 0 0 0
Otu231 0 0 0 0 0 0
Otu232 0 0 0 0 0 0
Otu233 0 0 0 0 0 0
Otu234 0 0 0 0 0 0
Otu235 0 0 0 0 12 0
Otu236 0 0 0 0 0 8
Otu237 0 0 0 0 0 0
Otu238 0 0 0 0 0 0
Otu239 0 0 0 0 0 0
Otu240 0 0 0 0 0 0
Otu241 0 0 0 0 0 0
Otu242 0 0 0 0 0 0
Otu243 0 0 0 0 0 22
Otu244 0 0 0 0 0 0
Otu245 0 0 0 0 0 0
Otu246 0 0 0 0 0 0
Otu247 0 0 0 0 0 0
Otu248 0 0 0 0 0 0
Otu249 0 0 0 0 0 0
Otu250 0 0 0 0 0 0
Otu251 0 0 0 0 0 0
Otu252 0 0 0 0 0 0
Otu253 0 0 0 0 0 0
Otu254 0 0 0 0 0 0
Otu255 0 0 0 0 0 0
Otu256 0 0 0 0 0 0
Otu257 0 0 0 0 0 0
Otu258 0 0 0 0 0 14
Otu259 0 0 0 0 0 0
Otu260 0 0 0 0 0 0
Otu261 0 0 0 0 0 18
Otu262 0 0 0 0 0 0
Otu263 0 0 0 0 0 0
Otu264 0 0 0 0 0 14
Otu265 0 0 0 0 0 0
Otu266 0 0 0 0 0 12
Otu267 0 0 0 0 0 0
Otu268 0 0 0 0 0 0
Otu269 0 0 0 0 0 0
Otu270 0 0 0 0 0 12
Otu271 0 0 0 0 0 0
Otu272 0 0 0 0 0 0
Otu273 0 0 0 0 0 0
Otu274 0 0 0 0 0 0
Otu275 0 0 0 0 0 0
Otu276 0 0 0 0 0 0
Otu277 0 0 0 0 0 0
Otu278 0 0 0 0 0 0
Otu279 0 0 0 0 0 0
Otu280 0 0 0 0 0 0
Otu281 0 0 0 0 0 0
Otu282 0 0 0 0 0 0
Otu283 0 0 0 0 0 0
Otu284 0 0 0 0 0 0
Otu285 0 0 0 0 0 0
Otu286 0 0 0 0 0 0
Otu287 0 0 0 0 0 0
In [ ]:
# definir los nombres de las filas de la columna tax
tax_mat <- tax_mat %>%
tibble::column_to_rownames("otu")
print(tax_mat)
Domain Supergroup Division Class
Otu001 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu002 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu003 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu004 Eukaryota Alveolata Dinophyta Dinophyceae
Otu005 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu006 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu007 Eukaryota Stramenopiles Ochrophyta Pelagophyceae
Otu008 Eukaryota Alveolata Dinophyta Dinophyceae
Otu009 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu010 Eukaryota Opisthokonta Metazoa Craniata
Otu011 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu012 Eukaryota Alveolata Dinophyta Dinophyceae
Otu013 Eukaryota Alveolata Dinophyta Syndiniales
Otu014 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu015 Eukaryota Alveolata Dinophyta Dinophyceae
Otu016 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu017 Eukaryota Opisthokonta Fungi Basidiomycota
Otu018 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu019 Eukaryota Opisthokonta Fungi Basidiomycota
Otu020 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu021 Eukaryota Alveolata Dinophyta Dinophyceae
Otu022 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu023 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu024 Eukaryota Archaeplastida Streptophyta Klebsormidiophyceae
Otu025 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu026 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu027 Eukaryota Alveolata Dinophyta Dinophyceae
Otu028 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu029 Eukaryota Opisthokonta Fungi Ascomycota
Otu030 Eukaryota Hacrobia Cryptophyta Cryptophyceae
Otu031 Eukaryota Alveolata Dinophyta Syndiniales
Otu032 Eukaryota Archaeplastida Chlorophyta Prasino_Clade_VII
Otu033 Eukaryota Archaeplastida Chlorophyta Ulvophyceae
Otu034 Eukaryota Alveolata Dinophyta Dinophyceae
Otu035 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu036 Eukaryota Hacrobia Haptophyta Haptophyta_HAP2
Otu037 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu038 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu039 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu040 Eukaryota Alveolata Dinophyta Dinophyceae
Otu041 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu042 Eukaryota Alveolata Dinophyta Dinophyceae
Otu043 Eukaryota Hacrobia Haptophyta Haptophyta_HAP3
Otu044 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu045 Eukaryota Stramenopiles Stramenopiles_X Bicoecea
Otu046 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu047 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu048 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu049 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu050 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu051 Eukaryota Opisthokonta Fungi Basidiomycota
Otu052 Eukaryota Archaeplastida Streptophyta Embryophyceae
Otu053 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu054 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu055 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu056 Eukaryota Alveolata Dinophyta Dinophyceae
Otu057 Eukaryota Archaeplastida Streptophyta Embryophyceae
Otu058 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu059 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu060 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu061 Eukaryota Alveolata Dinophyta Syndiniales
Otu062 Eukaryota Archaeplastida Chlorophyta Pyramimonadales
Otu063 Eukaryota Hacrobia Haptophyta Haptophyta_X
Otu064 Eukaryota Opisthokonta Fungi Ascomycota
Otu065 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu066 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu067 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu068 Eukaryota Alveolata Dinophyta Dinophyceae
Otu069 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu070 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu071 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu072 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu073 Eukaryota Stramenopiles Ochrophyta Pelagophyceae
Otu074 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu075 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu076 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu077 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu078 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu079 Eukaryota Alveolata Dinophyta Syndiniales
Otu080 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu081 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu082 Eukaryota Opisthokonta Choanoflagellida Choanoflagellatea
Otu083 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu084 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu085 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu086 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu087 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu088 Eukaryota Stramenopiles Ochrophyta Pelagophyceae
Otu089 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu090 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu091 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu092 Eukaryota Archaeplastida Chlorophyta Pyramimonadales
Otu093 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu094 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu095 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu096 Eukaryota Alveolata Dinophyta Dinophyceae
Otu097 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu098 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu099 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu100 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu101 Eukaryota Alveolata Dinophyta Dinophyceae
Otu102 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu103 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu104 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu105 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu106 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu107 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu108 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu109 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu110 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu111 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu112 Eukaryota Archaeplastida Streptophyta Embryophyceae
Otu113 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu114 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu115 Eukaryota Alveolata Dinophyta Dinophyceae
Otu116 Eukaryota Alveolata Dinophyta Syndiniales
Otu117 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu118 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu119 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu120 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu121 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu122 Eukaryota Opisthokonta Metazoa Arthropoda
Otu123 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu124 Eukaryota Opisthokonta Fungi Basidiomycota
Otu125 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu126 Eukaryota Hacrobia Cryptophyta Cryptophyceae
Otu127 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu128 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu129 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu130 Eukaryota Alveolata Dinophyta Dinophyceae
Otu131 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu132 Eukaryota Amoebozoa Lobosa Tubulinea
Otu133 Eukaryota Opisthokonta Fungi Basidiomycota
Otu134 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu135 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu136 Eukaryota Alveolata Dinophyta Dinophyceae
Otu137 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu138 Eukaryota Archaeplastida Streptophyta Embryophyceae
Otu139 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu140 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu141 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu142 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu143 Eukaryota Stramenopiles Stramenopiles_X Stramenopiles_X
Otu144 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu145 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu146 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu147 Eukaryota Stramenopiles Stramenopiles_X MAST
Otu148 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu149 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu150 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu151 Eukaryota Archaeplastida Chlorophyta Prasinococcales
Otu152 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu153 Eukaryota Alveolata Dinophyta Dinophyceae
Otu154 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu155 Eukaryota Hacrobia Telonemia Telonemia
Otu156 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu157 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu158 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu159 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu160 Eukaryota Opisthokonta Fungi Basidiomycota
Otu161 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu162 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu163 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu164 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu165 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu166 Eukaryota Opisthokonta Fungi Ascomycota
Otu167 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu168 Eukaryota Archaeplastida Chlorophyta Trebouxiophyceae
Otu169 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu170 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu171 Eukaryota Archaeplastida Chlorophyta Pyramimonadales
Otu172 Eukaryota Alveolata Dinophyta Syndiniales
Otu173 Eukaryota Opisthokonta Fungi Ascomycota
Otu174 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu175 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu176 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu177 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu178 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu179 Eukaryota Stramenopiles Ochrophyta Ochrophyta_X
Otu180 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu181 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu182 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu183 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu184 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu185 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu186 Eukaryota Archaeplastida Chlorophyta Prasino_Clade_IX
Otu187 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu188 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu189 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu190 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu191 Eukaryota Rhizaria Cercozoa Chlorarachniophyceae
Otu192 Eukaryota Archaeplastida Streptophyta Klebsormidiophyceae
Otu193 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu194 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu195 Eukaryota Opisthokonta Fungi Basidiomycota
Otu196 Eukaryota Alveolata Ciliophora Spirotrichea
Otu197 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu198 Eukaryota Opisthokonta Fungi Chytridiomycota
Otu199 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu200 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu201 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu202 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu203 Eukaryota Opisthokonta Fungi Basidiomycota
Otu204 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu205 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu206 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu207 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu208 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu209 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu210 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu211 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu212 Eukaryota Archaeplastida Streptophyta Klebsormidiophyceae
Otu213 Eukaryota Stramenopiles Ochrophyta Bolidophyceae
Otu214 Eukaryota Opisthokonta Fungi Basidiomycota
Otu215 Eukaryota Archaeplastida Chlorophyta Prasino_Clade_VII
Otu216 Eukaryota Alveolata Dinophyta Dinophyceae
Otu217 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu218 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu219 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu220 Eukaryota Archaeplastida Chlorophyta Prasinococcales
Otu221 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu222 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu223 Eukaryota Amoebozoa Lobosa Tubulinea
Otu224 Eukaryota Opisthokonta Fungi Basidiomycota
Otu225 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu226 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu227 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu228 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu229 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu230 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu231 Eukaryota Opisthokonta Fungi Ascomycota
Otu232 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu233 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu234 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu235 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu236 Eukaryota Hacrobia Cryptophyta Cryptophyceae
Otu237 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu238 Eukaryota Rhizaria Cercozoa Sarcomonadea
Otu239 Eukaryota Opisthokonta Metazoa Arthropoda
Otu240 Eukaryota Alveolata Dinophyta Syndiniales
Otu241 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu242 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu243 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu244 Eukaryota Stramenopiles Stramenopiles_X Stramenopiles_X
Otu245 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu246 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu247 Eukaryota Stramenopiles Ochrophyta Pelagophyceae
Otu248 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu249 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu250 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu251 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu252 Eukaryota Archaeplastida Chlorophyta Chlorophyceae
Otu253 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu254 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu255 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu256 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu257 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu258 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu259 Eukaryota Hacrobia Cryptophyta Cryptophyceae
Otu260 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu261 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu262 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu263 Eukaryota Alveolata Dinophyta Dinophyceae
Otu264 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu265 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu266 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu267 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu268 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu269 Eukaryota Alveolata Ciliophora Spirotrichea
Otu270 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu271 Eukaryota Hacrobia Centroheliozoa Centroheliozoa_X
Otu272 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu273 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu274 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu275 Eukaryota Stramenopiles Stramenopiles_X MOCH
Otu276 Eukaryota Stramenopiles Ochrophyta Dictyochophyceae
Otu277 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu278 Eukaryota Opisthokonta Metazoa Arthropoda
Otu279 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu280 Eukaryota Stramenopiles Ochrophyta Bacillariophyta
Otu281 Eukaryota Stramenopiles Ochrophyta Chrysophyceae
Otu282 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu283 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
Otu284 Eukaryota Archaeplastida Streptophyta Klebsormidiophyceae
Otu285 Eukaryota Alveolata Dinophyta Dinophyceae
Otu286 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
Otu287 Eukaryota Hacrobia Cryptophyta Cryptophyceae
Order Family
Otu001 Mamiellales Bathycoccaceae
Otu002 Prymnesiophyceae_X Braarudosphaeraceae
Otu003 Mamiellales Bathycoccaceae
Otu004 Dinophyceae_X Dinophyceae_X
Otu005 Mediophyceae Mediophyceae_X
Otu006 Bacillariophyceae Bacillariophyceae_X
Otu007 Pelagophyceae_X Pelagophyceae_X
Otu008 Dinophyceae_X Dinophyceae_X
Otu009 Prymnesiales Chrysochromulinaceae
Otu010 Craniata_X Craniata_XX
Otu011 Chrysophyceae_X Chrysophyceae_Clade_C
Otu012 Dinophyceae_X Dinophyceae_X
Otu013 Syndiniales_Group_III Syndiniales_Group_III_X
Otu014 Chrysophyceae_X Chrysophyceae_Clade_G
Otu015 Dinophyceae_X Dinophyceae_X
Otu016 Pterocystida Pterocystida_X
Otu017 Agaricomycotina Agaricomycetes
Otu018 Dictyochophyceae_X Pedinellales
Otu019 Agaricomycotina Agaricomycetes
Otu020 Prymnesiophyceae_X Braarudosphaeraceae
Otu021 Dinophyceae_X Dinophyceae_X
Otu022 Prymnesiophyceae_X Prymnesiophyceae_X
Otu023 Bacillariophyceae Bacillariophyceae_X
Otu024 Klebsormidiophyceae_X Klebsormidiophyceae_XX
Otu025 Mamiellales Mamiellaceae
Otu026 Bacillariophyceae Bacillariophyceae_X
Otu027 Suessiales Suessiales_X
Otu028 Isochrysidales Noelaerhabdaceae
Otu029 Saccharomycotina Saccharomycetales
Otu030 Cryptophyceae_X Cryptomonadales
Otu031 Syndiniales_Group_I Syndiniales_Group_I_Clade_1
Otu032 Prasino_Clade_VII_X Prasino_Clade_VII_A
Otu033 Ulvales_relatives Ulvales_relatives_X
Otu034 Dinophyceae_X Dinophyceae_X
Otu035 Chrysophyceae_X Chrysophyceae_Clade_G
Otu036 Haptophyta_HAP2 Haptophyta_HAP2
Otu037 Bacillariophyceae Bacillariophyceae_X
Otu038 Chrysophyceae_X Chrysophyceae_Clade_G
Otu039 Prymnesiophyceae_X Prymnesiophyceae_X
Otu040 Dinophyceae_X Dinophyceae_X
Otu041 Chrysophyceae_X Chrysophyceae_Clade_I
Otu042 Dinophyceae_X Dinophyceae_X
Otu043 Haptophyta_HAP3 Haptophyta_HAP3
Otu044 Mamiellales Mamiellaceae
Otu045 Borokales Borokaceae
Otu046 <NA> <NA>
Otu047 Dictyochophyceae_X Pedinellales
Otu048 Chrysophyceae_X Chrysophyceae_X
Otu049 MOCH_2 MOCH_2_X
Otu050 Chrysophyceae_X Chrysophyceae_Clade_H
Otu051 Ustilaginomycotina Exobasidiomycetes
Otu052 Embryophyceae_X Embryophyceae_XX
Otu053 Chrysophyceae_X Chrysophyceae_Clade_I
Otu054 MOCH_5 MOCH_5_X
Otu055 Prymnesiales Prymnesiales_X
Otu056 Dinophyceae_X Dinophyceae_X
Otu057 Embryophyceae_X Embryophyceae_XX
Otu058 Coccolithales Calcidiscaceae
Otu059 Bacillariophyceae Bacillariophyceae_X
Otu060 Dolichomastigales Crustomastigaceae
Otu061 Syndiniales_Group_III Syndiniales_Group_III_X
Otu062 Pyramimonadales_X Pyramimonadales_XX
Otu063 Haptophyta_X Haptophyta_X
Otu064 Saccharomycotina Saccharomycetales
Otu065 Prymnesiales Prymnesiales_Clade_B3
Otu066 Prymnesiophyceae_Clade_D Prymnesiophyceae_Clade_D_X
Otu067 Prymnesiales Chrysochromulinaceae
Otu068 Dinophyceae_X Dinophyceae_X
Otu069 Prymnesiales Chrysochromulinaceae
Otu070 Bacillariophyceae Bacillariophyceae_X
Otu071 Mediophyceae Mediophyceae_X
Otu072 Prymnesiales Prymnesiales_X
Otu073 Pelagophyceae_X Pelagophyceae_X
Otu074 Mediophyceae Mediophyceae_X
Otu075 Bacillariophyceae Bacillariophyceae_X
Otu076 Chrysophyceae_X Chrysophyceae_Clade_H
Otu077 Pterocystida Pterocystida_X
Otu078 Phaeocystales Phaeocystaceae
Otu079 Syndiniales_Group_II Syndiniales_Group_II_Clade_16
Otu080 Mediophyceae Mediophyceae_X
Otu081 Bacillariophyceae Bacillariophyceae_X
Otu082 Acanthoecida Stephanoecidae_Group_H
Otu083 Mediophyceae Mediophyceae_X
Otu084 MOCH_2 MOCH_2_X
Otu085 Mamiellales Mamiellaceae
Otu086 Chrysophyceae_X Chrysophyceae_Clade_C
Otu087 Coscinodiscophyceae Coscinodiscophyceae_X
Otu088 Pelagophyceae_X Pelagophyceae_X
Otu089 Mediophyceae Mediophyceae_X
Otu090 Bacillariophyceae Bacillariophyceae_X
Otu091 Bacillariophyta_X Bacillariophyta_X
Otu092 Pyramimonadales_X Pyramimonadales_XX
Otu093 MOCH_5 MOCH_5_X
Otu094 Calcihaptophycidae Calcihaptophycidae
Otu095 Prymnesiales Prymnesiales_Clade_B4
Otu096 Dinophyceae_X Dinophyceae_X
Otu097 Prymnesiophyceae_X Prymnesiophyceae_X
Otu098 Dictyochophyceae_X Pedinellales
Otu099 Prymnesiophyceae_X Prymnesiophyceae_X
Otu100 Mediophyceae Mediophyceae_X
Otu101 Dinophyceae_X Dinophyceae_X
Otu102 Chrysophyceae_X Chrysophyceae_Clade_C
Otu103 Prymnesiales Chrysochromulinaceae
Otu104 Phaeocystales Phaeocystaceae
Otu105 Dictyochophyceae_X Dictyochales
Otu106 Mediophyceae Mediophyceae_X
Otu107 Pterocystida Pterocystida_X
Otu108 <NA> <NA>
Otu109 Phaeocystales Phaeocystaceae
Otu110 Bacillariophyta_X Bacillariophyta_X
Otu111 Mediophyceae Mediophyceae_X
Otu112 Embryophyceae_X Embryophyceae_XX
Otu113 Dictyochophyceae_X Pedinellales
Otu114 Mamiellales Bathycoccaceae
Otu115 Dinophyceae_X Dinophyceae_X
Otu116 Syndiniales_Group_II Syndiniales_Group_II_Clade_10_and_11
Otu117 Chrysophyceae_X Chrysophyceae_Clade_I
Otu118 Prymnesiophyceae_X Prymnesiophyceae_X
Otu119 Mamiellales Mamiellaceae
Otu120 Mamiellales Bathycoccaceae
Otu121 Coscinodiscophyceae Coscinodiscophyceae_X
Otu122 Chelicerata Arachnida
Otu123 Mamiellales Bathycoccaceae
Otu124 Agaricomycotina Tremellomycetes
Otu125 Bacillariophyceae Bacillariophyceae_X
Otu126 Cryptophyceae_X Cryptomonadales
Otu127 Prymnesiales Prymnesiaceae
Otu128 Pterocystida Pterocystida_X
Otu129 Dictyochophyceae_X Florenciellales
Otu130 Dinophyceae_X Dinophyceae_X
Otu131 Mediophyceae Mediophyceae_X
Otu132 Echinamoebida Vermamoebidae
Otu133 Agaricomycotina Tremellomycetes
Otu134 Chrysophyceae_X Chrysophyceae_Clade_I
Otu135 Prymnesiophyceae_Clade_E Prymnesiophyceae_Clade_E_X
Otu136 Dinophyceae_X Dinophyceae_X
Otu137 Prymnesiophyceae_X Prymnesiophyceae_X
Otu138 Embryophyceae_X Embryophyceae_XX
Otu139 Isochrysidales Isochrysidaceae
Otu140 MOCH_1 MOCH_1_X
Otu141 Mamiellales Bathycoccaceae
Otu142 Mediophyceae Mediophyceae_X
Otu143 Stramenopiles_X Stramenopiles_X
Otu144 Dolichomastigales Dolichomastigaceae
Otu145 Pterocystida Pterocystida_X
Otu146 Prymnesiales Prymnesiaceae
Otu147 MAST_3 MAST_3D
Otu148 Phaeocystales Phaeocystaceae
Otu149 MOCH_2 MOCH_2_X
Otu150 Chrysophyceae_X Chrysophyceae_X
Otu151 Prasinococcales_X Prasinococcales_Clade_B
Otu152 Chrysophyceae_X Chrysophyceae_Clade_G
Otu153 Dinophyceae_X Dinophyceae_X
Otu154 Phaeocystales Phaeocystaceae
Otu155 Telonemia Telonemia_Group_2
Otu156 Mamiellales Bathycoccaceae
Otu157 Chrysophyceae_X Chrysophyceae_Clade_H
Otu158 Bacillariophyceae Bacillariophyceae_X
Otu159 MOCH_2 MOCH_2_X
Otu160 Ustilaginomycotina Exobasidiomycetes
Otu161 Pterocystida Pterocystida_X
Otu162 Dictyochophyceae_X Pedinellales
Otu163 MOCH_1 MOCH_1_X
Otu164 Pterocystida Pterocystida_X
Otu165 Bacillariophyceae Bacillariophyceae_X
Otu166 Saccharomycotina Saccharomycetales
Otu167 Coscinodiscophyceae Coscinodiscophyceae_X
Otu168 Chlorellales Chlorellales_X
Otu169 Pterocystida Pterocystida_X
Otu170 MOCH_2 MOCH_2_X
Otu171 Pyramimonadales_X Pyramimonadales_XX
Otu172 Syndiniales_Group_II Syndiniales_Group_II_Clade_14
Otu173 Saccharomycotina Saccharomycetales
Otu174 Chrysophyceae_X Chrysophyceae_Clade_G
Otu175 Bacillariophyta_X Bacillariophyta_X
Otu176 <NA> <NA>
Otu177 <NA> <NA>
Otu178 Mediophyceae Mediophyceae_X
Otu179 Ochrophyta_X Ochrophyta_X
Otu180 Prymnesiales Prymnesiaceae
Otu181 Chrysophyceae_X Chrysophyceae_Clade_C
Otu182 Mamiellales Bathycoccaceae
Otu183 Chrysophyceae_X Chrysophyceae_Clade_C
Otu184 Dictyochophyceae_X Florenciellales
Otu185 Mamiellales Bathycoccaceae
Otu186 Prasino_Clade_IX Prasino_Clade_IX_B
Otu187 Pterocystida Pterocystida_X
Otu188 Mamiellales Bathycoccaceae
Otu189 Chrysophyceae_X Chrysophyceae_Clade_C
Otu190 Dictyochophyceae_X Florenciellales
Otu191 Chlorarachnida Chlorarachnida_X
Otu192 Klebsormidiophyceae_X Klebsormidiophyceae_XX
Otu193 MOCH_1 MOCH_1_X
Otu194 Mediophyceae Mediophyceae_X
Otu195 Agaricomycotina Tremellomycetes
Otu196 Oligotrichia Strombidiidae
Otu197 MOCH_1 MOCH_1_X
Otu198 Chytridiomycotina Chytridiomycetes
Otu199 MOCH_2 MOCH_2_X
Otu200 Chrysophyceae_X Chrysophyceae_Clade_C
Otu201 Dictyochophyceae_X Dictyochales
Otu202 MOCH_5 MOCH_5_X
Otu203 Agaricomycotina Agaricomycetes
Otu204 Bacillariophytceae Bacillariaceae
Otu205 Bacillariophyceae Bacillariophyceae_X
Otu206 Chrysophyceae_X Chrysophyceae_Clade_G
Otu207 Mediophyceae Mediophyceae_X
Otu208 <NA> <NA>
Otu209 Mamiellales Bathycoccaceae
Otu210 Mamiellales Bathycoccaceae
Otu211 Mamiellales Mamiellaceae
Otu212 Klebsormidiophyceae_X Klebsormidiophyceae_XX
Otu213 Parmales Triparmaceae
Otu214 Agaricomycotina Agaricomycetes
Otu215 Prasino_Clade_VII_X Prasino_Clade_VII_B
Otu216 Dinophyceae_X Dinophyceae_X
Otu217 Chrysophyceae_X Chrysophyceae_Clade_G
Otu218 Mamiellales Bathycoccaceae
Otu219 Mamiellales Bathycoccaceae
Otu220 Prasinococcales_X Prasinococcales_Clade_B
Otu221 <NA> <NA>
Otu222 Mamiellales Bathycoccaceae
Otu223 Echinamoebida Vermamoebidae
Otu224 Agaricomycotina Agaricomycetes
Otu225 <NA> <NA>
Otu226 Coscinodiscophyceae Coscinodiscophyceae_X
Otu227 Mamiellales Bathycoccaceae
Otu228 Mamiellales Bathycoccaceae
Otu229 MOCH_1 MOCH_1_X
Otu230 Mamiellales Bathycoccaceae
Otu231 Saccharomycotina Saccharomycetales
Otu232 Bacillariophyceae Bacillariophyceae_X
Otu233 Bacillariophyta_X Bacillariophyta_X
Otu234 Mamiellales Bathycoccaceae
Otu235 Mamiellales Mamiellaceae
Otu236 Cryptophyceae_X Cryptomonadales
Otu237 Mamiellales Bathycoccaceae
Otu238 Glissomonadida Allapsidae
Otu239 Chelicerata Arachnida
Otu240 Syndiniales_Group_I Syndiniales_Group_I_Clade_1
Otu241 Mediophyceae Mediophyceae_X
Otu242 Mamiellales Bathycoccaceae
Otu243 Pterocystida Pterocystida_X
Otu244 Stramenopiles_X Stramenopiles_X
Otu245 Mamiellales Bathycoccaceae
Otu246 MOCH_5 MOCH_5_X
Otu247 Pelagophyceae_X Pelagophyceae_X
Otu248 Bacillariophytceae Bacillariaceae
Otu249 Mamiellales Mamiellaceae
Otu250 Dictyochophyceae_X Dictyochales
Otu251 Mamiellales Bathycoccaceae
Otu252 <NA> <NA>
Otu253 Mamiellales Bathycoccaceae
Otu254 Mamiellales Bathycoccaceae
Otu255 Bacillariophyta_X Bacillariophyta_X
Otu256 MOCH_5 MOCH_5_X
Otu257 Dictyochophyceae_X Pedinellales
Otu258 Pterocystida Pterocystida_X
Otu259 Cryptophyceae_X Cryptomonadales
Otu260 Bacillariophyta_X Bacillariophyta_X
Otu261 Pterocystida Pterocystida_X
Otu262 Pterocystida Pterocystida_X
Otu263 Dinophyceae_X Dinophyceae_X
Otu264 Pterocystida Pterocystida_X
Otu265 MOCH_2 MOCH_2_X
Otu266 Pterocystida Pterocystida_X
Otu267 Pterocystida Pterocystida_X
Otu268 Mamiellales Bathycoccaceae
Otu269 Choreotrichia Choreotrichia_X
Otu270 Pterocystida Pterocystida_X
Otu271 Pterocystida Pterocystida_X
Otu272 Mamiellales Mamiellaceae
Otu273 Mamiellales Mamiellaceae
Otu274 Prymnesiophyceae_X Braarudosphaeraceae
Otu275 MOCH_5 MOCH_5_X
Otu276 Dictyochophyceae_X Pedinellales
Otu277 Mamiellales Bathycoccaceae
Otu278 Chelicerata Arachnida
Otu279 Calcihaptophycidae Rhabdosphaeraceae
Otu280 Bacillariophyceae Bacillariophyceae_X
Otu281 Chrysophyceae_X Chrysophyceae_Clade_C
Otu282 Mamiellales Bathycoccaceae
Otu283 Mamiellales Bathycoccaceae
Otu284 Klebsormidiophyceae_X Klebsormidiophyceae_XX
Otu285 Dinophyceae_X Dinophyceae_X
Otu286 Isochrysidales Noelaerhabdaceae
Otu287 Cryptophyceae_X Cryptomonadales
Genus
Otu001 Ostreococcus
Otu002 UCYN_A1_host
Otu003 Bathycoccus
Otu004 Prorocentrum
Otu005 Thalassiosira
Otu006 Pseudo_nitzschia
Otu007 Pelagomonas
Otu008 Dinophyceae_X
Otu009 Chrysochromulina
Otu010 Craniata_XX_unclassified
Otu011 Chrysophyceae_Clade_C_X
Otu012 Gonyaulax
Otu013 Syndiniales_Group_III_X
Otu014 Chrysophyceae_Clade_G_X
Otu015 Dinophyceae_X
Otu016 Pterocystida_X
Otu017 Hyphodontia
Otu018 Pedinellales_X
Otu019 Itersonilia
Otu020 Braarudosphaera
Otu021 Dinophyceae_X
Otu022 Syracosphaera
Otu023 Bacillariophyceae_X
Otu024 Klebsormidium
Otu025 Micromonas
Otu026 Cylindrotheca
Otu027 Karlodinium
Otu028 Emiliania
Otu029 Debaryomyces
Otu030 Teleaulax
Otu031 Syndiniales_Group_I_Clade_1_X
Otu032 Prasino_Clade_VII_A_4_X
Otu033 Ulva
Otu034 Dinophyceae_X
Otu035 Chrysophyceae_Clade_G_X
Otu036 Haptophyta_HAP2_X
Otu037 Pseudo_nitzschia
Otu038 Chrysophyceae_Clade_G_X
Otu039 Algirosphaera
Otu040 Dinophyceae_X
Otu041 Chrysophyceae_Clade_I_X
Otu042 Dinophyceae_X
Otu043 Haptophyta_HAP3_X
Otu044 Micromonas
Otu045 Borokaceae_X
Otu046 Chlorophyceae_X
Otu047 Pedinellales_X
Otu048 Chrysophyceae_X
Otu049 MOCH_2_X
Otu050 Chrysophyceae_Clade_H_X
Otu051 Malassezia
Otu052 Allium
Otu053 Chrysophyceae_Clade_I_X
Otu054 MOCH_5_X
Otu055 Prymnesiales_X
Otu056 Dinophyceae_X
Otu057 Apium
Otu058 Oolithus
Otu059 Pseudo_nitzschia
Otu060 Crustomastix
Otu061 Syndiniales_Group_III_X
Otu062 Pyramimonas
Otu063 Haptophyta_X
Otu064 Saccharomycetales_unclassified
Otu065 Prymnesiales_Clade_B3_X
Otu066 Prymnesiophyceae_Clade_D_X
Otu067 Chrysochromulina
Otu068 Dinophyceae_X
Otu069 Chrysochromulina
Otu070 Bacillariophyceae_X
Otu071 Chaetoceros
Otu072 Prymnesiales_X
Otu073 Pelagophyceae_X
Otu074 Thalassiosira
Otu075 Nitzschia
Otu076 Chrysophyceae_Clade_H_X
Otu077 Pterocystida_X
Otu078 Phaeocystis
Otu079 Syndiniales_Group_II_Clade_16_X
Otu080 Chaetoceros
Otu081 Pseudo_nitzschia
Otu082 Stephanoecidae_Group_H_X
Otu083 Eucampia
Otu084 MOCH_2_X
Otu085 Micromonas
Otu086 Chrysophyceae_Clade_C_X
Otu087 Leptocylindrus
Otu088 Aureococcus
Otu089 Thalassiosira
Otu090 Bacillariophyceae_X
Otu091 Bacillariophyta_X
Otu092 Pterosperma
Otu093 MOCH_5_X
Otu094 Calcihaptophycidae_X
Otu095 Prymnesiales_Clade_B4_X
Otu096 Dinophyceae_X
Otu097 Syracosphaera/Algirosphaera
Otu098 Pedinellales_X
Otu099 Prymnesiophyceae_X
Otu100 Mediophyceae_X
Otu101 Dinophyceae_X
Otu102 Chrysophyceae_Clade_C_X
Otu103 Chrysochromulina
Otu104 Phaeocystis
Otu105 Dictyochales_X
Otu106 Mediophyceae_X
Otu107 Pterocystida_X
Otu108 Chlorophyceae_X
Otu109 Phaeocystis
Otu110 Bacillariophyta_X
Otu111 Chaetoceros
Otu112 Lycopersicon
Otu113 Pseudopedinella
Otu114 Ostreococcus
Otu115 Dinophyceae_X
Otu116 Syndiniales_Group_II_Clade_10_and_11_X
Otu117 Chrysophyceae_Clade_I_X
Otu118 Prymnesiophyceae_X
Otu119 Mantoniella
Otu120 Bathycoccus
Otu121 Guinardia
Otu122 Demodex
Otu123 Ostreococcus
Otu124 Tremellomycetes_unclassified
Otu125 Bacillariophyceae_X
Otu126 Teleaulax
Otu127 Prymnesium
Otu128 Pterocystida_X
Otu129 Florenciella
Otu130 Dinophyceae_X
Otu131 Thalassiosira
Otu132 Vermamoeba
Otu133 Filobasidium
Otu134 Chrysophyceae_Clade_I_X
Otu135 Prymnesiophyceae_Clade_E_X
Otu136 Prorocentrum
Otu137 Phaeocystis
Otu138 Citrus
Otu139 Tisochrysis
Otu140 MOCH_1_X
Otu141 Ostreococcus
Otu142 Mediophyceae_X
Otu143 Stramenopiles_X
Otu144 Dolichomastix
Otu145 Pterocystida_X
Otu146 Dicrateria
Otu147 MAST_3D_X
Otu148 Phaeocystis
Otu149 MOCH_2_X
Otu150 Chrysophyceae_X
Otu151 Prasinoderma
Otu152 Chrysophyceae_Clade_G_X
Otu153 Dinophyceae_X
Otu154 Phaeocystis
Otu155 Telonemia_Group_2_X
Otu156 Bathycoccus
Otu157 Chrysophyceae_Clade_H_X
Otu158 Pseudo_nitzschia
Otu159 MOCH_2_X
Otu160 Malassezia
Otu161 Pterocystida_X
Otu162 Helicopedinella
Otu163 MOCH_1_X
Otu164 Pterocystida_X
Otu165 Pseudo_nitzschia
Otu166 Hanseniaspora
Otu167 Leptocylindrus
Otu168 Picochlorum
Otu169 Pterocystida_X
Otu170 MOCH_2_X
Otu171 Halosphaera
Otu172 Syndiniales_Group_II_Clade_14_X
Otu173 Candida
Otu174 Chrysophyceae_Clade_G_X
Otu175 Bacillariophyta_X
Otu176 Chlorophyceae_X
Otu177 Chlorophyceae_X
Otu178 Thalassiosira
Otu179 Ochrophyta_X
Otu180 Prymnesium
Otu181 Chrysophyceae_Clade_C_X
Otu182 Bathycoccus
Otu183 Chrysophyceae_Clade_C_X
Otu184 Florenciellales_X
Otu185 Bathycoccus
Otu186 Prasino_Clade_IX_B_X
Otu187 Pterocystida_X
Otu188 Bathycoccus
Otu189 Chrysophyceae_Clade_C_X
Otu190 Florenciella
Otu191 Bigelowiella
Otu192 Klebsormidium
Otu193 MOCH_1_X
Otu194 Mediophyceae_X
Otu195 Tremellomycetes_unclassified
Otu196 Pseudotontonia
Otu197 MOCH_1_X
Otu198 Chytridiomycetes_X
Otu199 MOCH_2_X
Otu200 Chrysophyceae_Clade_C_X
Otu201 Dictyochales_X
Otu202 MOCH_5_X
Otu203 Agaricomycetes_unclassified
Otu204 Fragilariopsis
Otu205 Pseudo_nitzschia
Otu206 Chrysophyceae_Clade_G_X
Otu207 Chaetoceros
Otu208 Chlorophyceae_X
Otu209 Ostreococcus
Otu210 Ostreococcus
Otu211 Micromonas
Otu212 Klebsormidium
Otu213 Triparma
Otu214 Lentinula
Otu215 Prasino_Clade_VII_B_1_X
Otu216 Gonyaulax
Otu217 Chrysophyceae_Clade_G_X
Otu218 Ostreococcus
Otu219 Bathycoccus
Otu220 Prasinococcales_Clade_B_X
Otu221 Chlorophyceae_X
Otu222 Ostreococcus
Otu223 Vermamoeba
Otu224 Trametes
Otu225 Chlorophyceae_X
Otu226 Leptocylindrus
Otu227 Bathycoccus
Otu228 Ostreococcus
Otu229 MOCH_1_X
Otu230 Ostreococcus
Otu231 Yarrowia
Otu232 Pseudo_nitzschia
Otu233 Bacillariophyta_X
Otu234 Bathycoccus
Otu235 Micromonas
Otu236 Hemiselmis
Otu237 Ostreococcus
Otu238 Allapsidae_X
Otu239 Demodex
Otu240 Syndiniales_Group_I_Clade_1_X
Otu241 Mediophyceae_X
Otu242 Bathycoccus
Otu243 Pterocystida_X
Otu244 Stramenopiles_X
Otu245 Ostreococcus
Otu246 MOCH_5_X
Otu247 Aureococcus
Otu248 Fragilariopsis
Otu249 Micromonas
Otu250 Dictyochales_X
Otu251 Ostreococcus
Otu252 Chlorophyceae_X
Otu253 Bathycoccus
Otu254 Bathycoccus
Otu255 Bacillariophyta_X
Otu256 MOCH_5_X
Otu257 Pedinellales_X
Otu258 Pterocystida_X
Otu259 Teleaulax
Otu260 Bacillariophyta_X
Otu261 Pterocystida_X
Otu262 Pterocystida_X
Otu263 Dinophyceae_X
Otu264 Pterocystida_X
Otu265 MOCH_2_X
Otu266 Pterocystida_X
Otu267 Pterocystida_X
Otu268 Bathycoccus
Otu269 Choreotrichia_X
Otu270 Pterocystida_X
Otu271 Pterocystida_X
Otu272 Micromonas
Otu273 Micromonas
Otu274 UCYN_A1_host
Otu275 MOCH_5_X
Otu276 Pedinellales_X
Otu277 Ostreococcus
Otu278 Tyrophagus
Otu279 Algirosphaera
Otu280 Pseudo_nitzschia
Otu281 Chrysophyceae_Clade_C_X
Otu282 Ostreococcus
Otu283 Bathycoccus
Otu284 Klebsormidium
Otu285 Dinophyceae_X
Otu286 Emiliania
Otu287 Teleaulax
In [ ]:
# definir los nombres de las filas de la columna samples
samples_df <- samples_df %>%
tibble::column_to_rownames("sample")
In [ ]:
# Transformar en matrices otu y tablas de tax (la tabla de muestra se puede dejar como marco de datos)
otu_mat <- as.matrix(otu_mat)
tax_mat <- as.matrix(tax_mat)
In [ ]:
# Transformar a objetos phyloseq
conflicts_prefer(MicrobiotaProcess::tax_table)
conflicts_prefer(phyloseq::tax_table)
OTU = otu_table(otu_mat, taxa_are_rows = TRUE)
OTU
TAX = tax_table(tax_mat)
TAX
samples = sample_data(samples_df)
samples
# manejamos en un solo ojbeto los datos anteriormente transformados
carbom <- phyloseq(OTU, TAX, samples)
carbom
[conflicted] Removing existing preference. [conflicted] Will prefer MicrobiotaProcess::tax_table over any other package.
[conflicted] Removing existing preference. [conflicted] Will prefer phyloseq::tax_table over any other package.
| X10n | X10p | X11n | X11p | X120n | X120p | X121n | X121p | X122n | X122p | ... | X7n | X7p | X9n | X9p | tri01n | tri01p | tri02n | tri02p | tri03n | tri03p | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Otu001 | 13679 | 6292 | 42 | 2500 | 18850 | 5 | 43 | 7138 | 9432 | 10541 | ... | 12541 | 651 | 6453 | 9453 | 0 | 27 | 49 | 4 | 30 | 3 |
| Otu002 | 18 | 7134 | 38 | 9830 | 45 | 61420 | 182 | 23751 | 36 | 11 | ... | 10010 | 16 | 1666 | 23 | 2719 | 11974 | 6067 | 2827 | 52 | 17261 |
| Otu003 | 9939 | 8983 | 31 | 13 | 24620 | 19 | 19 | 16 | 12502 | 3831 | ... | 23 | 8 | 4933 | 8939 | 0 | 25 | 45 | 7 | 12 | 3 |
| Otu004 | 3675 | 4234 | 24 | 22 | 11 | 16 | 32967 | 35 | 6 | 18 | ... | 8 | 14922 | 6 | 12 | 5 | 0 | 3 | 0 | 3 | 8 |
| Otu005 | 0 | 5 | 0 | 7 | 0 | 8 | 0 | 16 | 20166 | 0 | ... | 15 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 13 |
| Otu006 | 0 | 8 | 0 | 0 | 0 | 8 | 0 | 0 | 5 | 3 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 0 | 0 |
| Otu007 | 4587 | 518 | 4 | 386 | 8775 | 5 | 6 | 1102 | 14336 | 0 | ... | 9 | 3 | 1 | 7972 | 0 | 11 | 4 | 1 | 0 | 18 |
| Otu008 | 1 | 8 | 2 | 4408 | 3 | 29 | 6 | 12355 | 0 | 0 | ... | 762 | 2 | 0 | 752 | 0 | 0 | 0 | 8 | 5412 | 8 |
| Otu009 | 115 | 914 | 3 | 325 | 0 | 629 | 1 | 834 | 5 | 0 | ... | 1520 | 675 | 64 | 3 | 2 | 14476 | 5 | 0 | 0 | 695 |
| Otu010 | 780 | 8 | 23810 | 12 | 3279 | 0 | 12 | 7 | 3027 | 0 | ... | 0 | 0 | 1 | 5860 | 1385 | 5 | 2 | 7 | 19278 | 9 |
| Otu011 | 0 | 3 | 2 | 2 | 0 | 13 | 5 | 5 | 4 | 7 | ... | 0 | 0 | 1 | 7696 | 0 | 8 | 0 | 0 | 3 | 0 |
| Otu012 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 16 | 3 | 0 | ... | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 |
| Otu013 | 6321 | 2471 | 2 | 0 | 12 | 3 | 0 | 0 | 4 | 20272 | ... | 2 | 12 | 893 | 4 | 0 | 0 | 4 | 1 | 0 | 0 |
| Otu014 | 0 | 82 | 4 | 3304 | 1 | 1667 | 4 | 9233 | 13 | 3 | ... | 2637 | 0 | 1 | 5 | 5 | 5 | 6 | 5 | 2 | 8 |
| Otu015 | 0 | 12 | 0 | 3 | 7 | 25 | 1 | 6 | 10 | 0 | ... | 3 | 0 | 1155 | 5 | 4 | 1 | 0 | 0 | 0 | 0 |
| Otu016 | 1 | 0 | 0 | 9 | 5 | 0 | 0 | 14 | 0 | 0 | ... | 1 | 0 | 325 | 0 | 2 | 4 | 10 | 5 | 7 | 32443 |
| Otu017 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 17 | 8 | ... | 10 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu018 | 1 | 0 | 9 | 911 | 0 | 0 | 15 | 2702 | 6 | 4 | ... | 2104 | 7 | 1 | 0 | 0 | 1 | 1 | 0 | 13 | 0 |
| Otu019 | 0 | 0 | 13 | 0 | 0 | 0 | 29 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 |
| Otu020 | 425 | 0 | 1 | 0 | 1706 | 0 | 8447 | 1 | 0 | 0 | ... | 1 | 1267 | 0 | 431 | 0 | 2191 | 0 | 0 | 0 | 0 |
| Otu021 | 0 | 4 | 0 | 0 | 0 | 10 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 3 | 0 | 1 | 0 | 0 | 9 | 0 | 0 |
| Otu022 | 0 | 0 | 0 | 4987 | 0 | 0 | 0 | 6 | 90 | 1 | ... | 6 | 4 | 0 | 0 | 0 | 5 | 0 | 4 | 5 | 8 |
| Otu023 | 4 | 0 | 1 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | ... | 2053 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 2 | 399 |
| Otu024 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 8 | 0 | 9 | 0 | 0 | 0 | 0 |
| Otu025 | 69 | 0 | 0 | 0 | 290 | 0 | 0 | 0 | 21 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 6472 | 0 |
| Otu026 | 0 | 2 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 1 | ... | 0 | 2 | 0 | 0 | 192 | 7767 | 2 | 13547 | 3 | 5 |
| Otu027 | 6 | 2304 | 0 | 0 | 5 | 0 | 0 | 0 | 57 | 4 | ... | 0 | 1 | 0 | 7 | 0 | 12 | 6 | 0 | 0 | 0 |
| Otu028 | 19 | 467 | 0 | 363 | 79 | 0 | 1 | 816 | 1 | 0 | ... | 91 | 1 | 0 | 2242 | 0 | 13 | 4924 | 0 | 2 | 5 |
| Otu029 | 0 | 1271 | 0 | 1 | 0 | 0 | 1794 | 1 | 1762 | 929 | ... | 1 | 12 | 0 | 0 | 3 | 0 | 2 | 0 | 1 | 3 |
| Otu030 | 0 | 5 | 0 | 0 | 0 | 4 | 0 | 0 | 155 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | |
| Otu258 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 |
| Otu259 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu260 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu261 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 18 |
| Otu262 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu263 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu264 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 |
| Otu265 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 10 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu266 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 |
| Otu267 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu268 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu269 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu270 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 |
| Otu271 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu272 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu273 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu274 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu275 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu276 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu277 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 | 0 | ... | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu278 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu279 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu280 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu281 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu282 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu283 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu284 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu285 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu286 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otu287 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Domain | Supergroup | Division | Class | Order | Family | Genus | |
|---|---|---|---|---|---|---|---|
| Otu001 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu002 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | UCYN_A1_host |
| Otu003 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu004 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Prorocentrum |
| Otu005 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Mediophyceae | Mediophyceae_X | Thalassiosira |
| Otu006 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Pseudo_nitzschia |
| Otu007 | Eukaryota | Stramenopiles | Ochrophyta | Pelagophyceae | Pelagophyceae_X | Pelagophyceae_X | Pelagomonas |
| Otu008 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu009 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiales | Chrysochromulinaceae | Chrysochromulina |
| Otu010 | Eukaryota | Opisthokonta | Metazoa | Craniata | Craniata_X | Craniata_XX | Craniata_XX_unclassified |
| Otu011 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_C | Chrysophyceae_Clade_C_X |
| Otu012 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Gonyaulax |
| Otu013 | Eukaryota | Alveolata | Dinophyta | Syndiniales | Syndiniales_Group_III | Syndiniales_Group_III_X | Syndiniales_Group_III_X |
| Otu014 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_G | Chrysophyceae_Clade_G_X |
| Otu015 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu016 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu017 | Eukaryota | Opisthokonta | Fungi | Basidiomycota | Agaricomycotina | Agaricomycetes | Hyphodontia |
| Otu018 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Pedinellales | Pedinellales_X |
| Otu019 | Eukaryota | Opisthokonta | Fungi | Basidiomycota | Agaricomycotina | Agaricomycetes | Itersonilia |
| Otu020 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | Braarudosphaera |
| Otu021 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu022 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Prymnesiophyceae_X | Syracosphaera |
| Otu023 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Bacillariophyceae_X |
| Otu024 | Eukaryota | Archaeplastida | Streptophyta | Klebsormidiophyceae | Klebsormidiophyceae_X | Klebsormidiophyceae_XX | Klebsormidium |
| Otu025 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu026 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Cylindrotheca |
| Otu027 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Suessiales | Suessiales_X | Karlodinium |
| Otu028 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Isochrysidales | Noelaerhabdaceae | Emiliania |
| Otu029 | Eukaryota | Opisthokonta | Fungi | Ascomycota | Saccharomycotina | Saccharomycetales | Debaryomyces |
| Otu030 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
| ... | ... | ... | ... | ... | ... | ... | ... |
| Otu258 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu259 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
| Otu260 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyta_X | Bacillariophyta_X | Bacillariophyta_X |
| Otu261 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu262 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu263 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu264 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu265 | Eukaryota | Stramenopiles | Stramenopiles_X | MOCH | MOCH_2 | MOCH_2_X | MOCH_2_X |
| Otu266 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu267 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu268 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu269 | Eukaryota | Alveolata | Ciliophora | Spirotrichea | Choreotrichia | Choreotrichia_X | Choreotrichia_X |
| Otu270 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu271 | Eukaryota | Hacrobia | Centroheliozoa | Centroheliozoa_X | Pterocystida | Pterocystida_X | Pterocystida_X |
| Otu272 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu273 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu274 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | UCYN_A1_host |
| Otu275 | Eukaryota | Stramenopiles | Stramenopiles_X | MOCH | MOCH_5 | MOCH_5_X | MOCH_5_X |
| Otu276 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Pedinellales | Pedinellales_X |
| Otu277 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu278 | Eukaryota | Opisthokonta | Metazoa | Arthropoda | Chelicerata | Arachnida | Tyrophagus |
| Otu279 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Calcihaptophycidae | Rhabdosphaeraceae | Algirosphaera |
| Otu280 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Pseudo_nitzschia |
| Otu281 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_C | Chrysophyceae_Clade_C_X |
| Otu282 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu283 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu284 | Eukaryota | Archaeplastida | Streptophyta | Klebsormidiophyceae | Klebsormidiophyceae_X | Klebsormidiophyceae_XX | Klebsormidium |
| Otu285 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu286 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Isochrysidales | Noelaerhabdaceae | Emiliania |
| Otu287 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
| fraction | Select_18S_nifH | total_18S | total_16S | total_nifH | sample_number | transect | station | depth | latitude | ... | phosphates | silicates | ammonia | nitrates | nitrites | temperature | fluorescence | salinity | sample_label | costa | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <chr> | <dbl> | <chr> | <dbl> | <dbl> | ... | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | |
| X10n | Nano | Yes | 53230 | 8772 | 36 | 10 | 1 | 81 | 140 | -27.42 | ... | 0.2 | 1.64 | 0 | 0.26 | 7.0000000000000007E-2 | 17.3 | 553.79999999999995 | 35.9 | TR1_St81_140m_10n | Sergipe |
| X10p | Pico | Yes | 47390 | 4448 | 6241 | 10 | 1 | 81 | 140 | -27.42 | ... | 0.2 | 1.64 | 0 | 0.26 | 7.0000000000000007E-2 | 17.3 | 553.79999999999995 | 35.9 | TR1_St81_140m_10p | Sergipe |
| X11n | Nano | No | 24007 | 6193 | 3772 | 11 | 1 | 85 | 110 | -26.80 | ... | 0.28999999999999998 | 1.58 | 0 | 0.22 | 0.05 | 21.3 | 397.5 | 36.5 | TR1_St85_110m_11n | Esp<U+00ED>rito Santo |
| X11p | Pico | Yes | 31899 | 14 | 10201 | 11 | 1 | 85 | 110 | -26.80 | ... | 0.28999999999999998 | 1.58 | 0 | 0.22 | 0.05 | 21.3 | 397.5 | 36.5 | TR1_St85_110m_11p | Esp<U+00ED>rito Santo |
| X120n | Nano | Yes | 70455 | 5292 | 93 | 120 | 2 | 96 | 5 | -27.39 | ... | 0.43 | 4 | 0 | 0.19 | 0.14000000000000001 | 23.1 | 149.30000000000001 | 33.5 | TR2_St96_5m_120n | Esp<U+00ED>rito Santo |
| X120p | Pico | Yes | 76182 | 53272 | 23147 | 120 | 2 | 96 | 5 | -27.39 | ... | 0.43 | 4 | 0 | 0.19 | 0.14000000000000001 | 23.1 | 149.30000000000001 | 33.5 | TR2_St96_5m_120p | Esp<U+00ED>rito Santo |
| X121n | Nano | Yes | 52401 | 5958 | 26838 | 121 | 2 | 96 | 30 | -27.39 | ... | 0.43 | 3.89 | 0.04 | 0.23 | 0.09 | 22.6 | 223.9 | 33.700000000000003 | TR2_St96_30m_121n | Bah<U+00ED>a |
| X121p | Pico | Yes | 71785 | 10993 | 23706 | 121 | 2 | 96 | 30 | -27.39 | ... | 0.43 | 3.89 | 0.04 | 0.23 | 0.09 | 22.6 | 223.9 | 33.700000000000003 | TR2_St96_30m_121p | Bah<U+00ED>a |
| X122n | Nano | Yes | 78740 | 11730 | 15543 | 122 | 2 | 96 | 50 | -27.39 | ... | 0.56000000000000005 | 6.59 | 0.04 | 0.21 | 7.0000000000000007E-2 | 20.3 | 779.6 | 35.9 | TR2_St96_50m_122n | R<U+00ED>o de Janeiro |
| X122p | Pico | Yes | 37364 | 11817 | 11045 | 122 | 2 | 96 | 50 | -27.39 | ... | 0.56000000000000005 | 6.59 | 0.04 | 0.21 | 7.0000000000000007E-2 | 20.3 | 779.6 | 35.9 | TR2_St96_50m_122p | R<U+00ED>o de Janeiro |
| X125n | Nano | Yes | 27381 | 9 | 14331 | 125 | 2 | 98 | 5 | -27.59 | ... | 0.28999999999999998 | 1.86 | 0.04 | 0.25 | 7.0000000000000007E-2 | 23.1 | 89.3 | 35.700000000000003 | TR2_St98_5m_125n | R<U+00ED>o de Janeiro |
| X125p | Pico | Yes | 55179 | 10419 | 21461 | 125 | 2 | 98 | 5 | -27.59 | ... | 0.28999999999999998 | 1.86 | 0.04 | 0.25 | 7.0000000000000007E-2 | 23.1 | 89.3 | 35.700000000000003 | TR2_St98_5m_125p | R<U+00ED>o de Janeiro |
| X126n | Nano | Yes | 65714 | 15 | 16929 | 126 | 2 | 98 | 50 | -27.59 | ... | 0.25 | 0.98 | 0 | 0.2 | 0.12 | 23.7 | 113.2 | 37.200000000000003 | TR2_St98_50m_126n | R<U+00ED>o de Janeiro |
| X126p | Pico | Yes | 30406 | 3 | 10140 | 126 | 2 | 98 | 50 | -27.59 | ... | 0.25 | 0.98 | 0 | 0.2 | 0.12 | 23.7 | 113.2 | 37.200000000000003 | TR2_St98_50m_126p | R<U+00ED>o de Janeiro |
| X127n | Nano | Yes | 60610 | 9 | 11493 | 127 | 2 | 98 | 85 | -27.59 | ... | 0.25 | 1.03 | 0 | 0.47 | 0.26 | 22.9 | 427.5 | 37 | TR2_St98_85m_127n | Bah<U+00ED>a |
| X13n | Nano | Yes | 46001 | 33 | 21316 | 13 | 1 | 86 | 105 | -26.33 | ... | 0.34 | 1.0900000000000001 | 0.04 | 0.15 | 0.26 | 20.9 | 425.6 | 36.299999999999997 | TR1_St86_105m_13n | Bah<U+00ED>a |
| X13p | Pico | Yes | 59626 | 7217 | 11954 | 13 | 1 | 86 | 105 | -26.33 | ... | 0.34 | 1.0900000000000001 | 0.04 | 0.15 | 0.26 | 20.9 | 425.6 | 36.299999999999997 | TR1_St86_105m_13p | Bah<U+00ED>a |
| X140n | Nano | Yes | 48126 | 10428 | 25286 | 140 | 2 | 101 | 5 | -27.79 | ... | 0.28999999999999998 | 1.2 | 0 | 0.14000000000000001 | 0.05 | 23.5 | 54 | 36.5 | TR2_St101_5m_140n | Bah<U+00ED>a |
| X140p | Pico | Yes | 46569 | 10448 | 12301 | 140 | 2 | 101 | 5 | -27.79 | ... | 0.28999999999999998 | 1.2 | 0 | 0.14000000000000001 | 0.05 | 23.5 | 54 | 36.5 | TR2_St101_5m_140p | Bah<U+00ED>a |
| X141n | Nano | Yes | 30081 | 6394 | 21302 | 141 | 2 | 101 | 60 | -27.79 | ... | 0.25 | 1.03 | 0 | 0.22 | 0.09 | 23.7 | 106.5 | 37.200000000000003 | TR2_St101_60m_141n | Bah<U+00ED>a |
| X141p | Pico | Yes | 64221 | 11318 | 10428 | 141 | 2 | 101 | 60 | -27.79 | ... | 0.25 | 1.03 | 0 | 0.22 | 0.09 | 23.7 | 106.5 | 37.200000000000003 | TR2_St101_60m_141p | Bah<U+00ED>a |
| X142n | Nano | Yes | 85219 | 23243 | 11753 | 142 | 2 | 101 | 110 | -27.79 | ... | 0.28999999999999998 | 1.0900000000000001 | 0 | 0.84 | 0.23 | 23.3 | 373 | 37.1 | TR2_St101_110m_142n | Bah<U+00ED>a |
| X142p | Pico | Yes | 89797 | 9553 | 17156 | 142 | 2 | 101 | 110 | -27.79 | ... | 0.28999999999999998 | 1.0900000000000001 | 0 | 0.84 | 0.23 | 23.3 | 373 | 37.1 | TR2_St101_110m_142p | Sergipe |
| X155n | Nano | Yes | 54162 | 8237 | 20674 | 155 | 2 | 106 | 5 | -28.12 | ... | 0.25 | 1.03 | 0 | 0.37 | 0.09 | 23 | 55.3 | 36.9 | TR2_St106_5m_155n | Sergipe |
| X155p | Pico | Yes | 50782 | 7384 | 66172 | 155 | 2 | 106 | 5 | -28.12 | ... | 0.25 | 1.03 | 0 | 0.37 | 0.09 | 23 | 55.3 | 36.9 | TR2_St106_5m_155p | Sergipe |
| X156n | Nano | Yes | 55065 | 11371 | 14447 | 156 | 2 | 106 | 60 | -28.12 | ... | 0.25 | 1.03 | 0 | 0.34 | 7.0000000000000007E-2 | 22.9 | 98.5 | 36.9 | TR2_St106_60m_156n | Sergipe |
| X156p | Pico | Yes | 43917 | 9665 | 16093 | 156 | 2 | 106 | 60 | -28.12 | ... | 0.25 | 1.03 | 0 | 0.34 | 7.0000000000000007E-2 | 22.9 | 98.5 | 36.9 | TR2_St106_60m_156p | Sergipe |
| X157n | Nano | Yes | 29078 | 4978 | 15532 | 157 | 2 | 106 | 100 | -28.12 | ... | 0.28999999999999998 | 0.98 | 0 | 0.4 | 7.0000000000000007E-2 | 21.5 | 413.2 | 36.700000000000003 | TR2_St106_100m_157n | Sergipe |
| X157p | Pico | Yes | 51848 | 9139 | 15204 | 157 | 2 | 106 | 100 | -28.12 | ... | 0.28999999999999998 | 0.98 | 0 | 0.4 | 7.0000000000000007E-2 | 21.5 | 413.2 | 36.700000000000003 | TR2_St106_100m_157p | Sergipe |
| X15n | Nano | Yes | 22468 | 2887 | 2678 | 15 | 1 | 87 | 105 | -26.22 | ... | 0.47 | 1.47 | 0 | 1.51 | 0.46 | 19.5 | 473.7 | 36.1 | TR1_St87_105m_15n | Sergipe |
| X15p | Pico | Yes | 78390 | 13813 | 1033 | 15 | 1 | 87 | 105 | -26.22 | ... | 0.47 | 1.47 | 0 | 1.51 | 0.46 | 19.5 | 473.7 | 36.1 | TR1_St87_105m_15p | R<U+00ED>o de Janeiro |
| X165n | Nano | Yes | 50732 | 15337 | 14706 | 165 | 2 | 114 | 5 | -28.65 | ... | 0.28999999999999998 | 1.36 | 0.09 | 0.28000000000000003 | 0.05 | 22.4 | 54.2 | 36.4 | TR2_St114_5m_165n | R<U+00ED>o de Janeiro |
| X165p | Pico | Yes | 48514 | 10902 | 39918 | 165 | 2 | 114 | 5 | -28.65 | ... | 0.28999999999999998 | 1.36 | 0.09 | 0.28000000000000003 | 0.05 | 22.4 | 54.2 | 36.4 | TR2_St114_5m_165p | R<U+00ED>o de Janeiro |
| X166n | Nano | Yes | 53412 | 3411 | 24442 | 166 | 2 | 114 | 60 | -28.65 | ... | 0.16 | 0.98 | 0 | 0.25 | 7.0000000000000007E-2 | 21.4 | 75.900000000000006 | 36.6 | TR2_St114_60m_166n | R<U+00ED>o de Janeiro |
| X166p | Pico | Yes | 62897 | 12788 | 28107 | 166 | 2 | 114 | 60 | -28.65 | ... | 0.16 | 0.98 | 0 | 0.25 | 7.0000000000000007E-2 | 21.4 | 75.900000000000006 | 36.6 | TR2_St114_60m_166p | R<U+00ED>o de Janeiro |
| X167n | Nano | Yes | 31424 | 12874 | 20616 | 167 | 2 | 114 | 80 | -28.65 | ... | 0.2 | 0.98 | 0 | 0.21 | 0.02 | 21 | 242.9 | 36.6 | TR2_St114_80m_167n | R<U+00ED>o de Janeiro |
| X167p | Pico | Yes | 49934 | 10885 | 13971 | 167 | 2 | 114 | 80 | -28.65 | ... | 0.2 | 0.98 | 0 | 0.21 | 0.02 | 21 | 242.9 | 36.6 | TR2_St114_80m_167p | Bah<U+00ED>a |
| X1n | Nano | Yes | 95054 | 9139 | 163 | 1 | 0 | 6 | 45 | -23.58 | ... | 0.47 | 1.03 | 0 | 1.07 | 0.24 | 19.7 | 2773.75 | 36.299999999999997 | TR0_St6_45m_1n | Bah<U+00ED>a |
| X1p | Pico | Yes | 19466 | 15987 | 137117 | 1 | 0 | 6 | 45 | -23.58 | ... | 0.47 | 1.03 | 0 | 1.07 | 0.24 | 19.7 | 2773.75 | 36.299999999999997 | TR0_St6_45m_1p | Bah<U+00ED>a |
| X2n | Nano | Yes | 45111 | 10029 | 143 | 2 | 0 | 6 | 45 | -23.58 | ... | 0.47 | 1.03 | 0 | 1.07 | 0.24 | 19.7 | 2773.75 | 36.299999999999997 | TR0_St6_45m_2n | Esp<U+00ED>rito Santo |
| X2p | Pico | Yes | 107644 | 14585 | 113897 | 2 | 0 | 6 | 45 | -23.58 | ... | 0.47 | 1.03 | 0 | 1.07 | 0.24 | 19.7 | 2773.75 | 36.299999999999997 | TR0_St6_45m_2p | Esp<U+00ED>rito Santo |
| X3n | Nano | Yes | 131031 | 10037 | 116 | 3 | 0 | 19 | 5 | -25.79 | ... | 0.28999999999999998 | 1.31 | 0.04 | 0.48 | 0.02 | 22.7 | 37 | 36.9 | TR0_St19_5m_3n | Esp<U+00ED>rito Santo |
| X3p | Pico | Yes | 134873 | 26 | 92500 | 3 | 0 | 19 | 5 | -25.79 | ... | 0.28999999999999998 | 1.31 | 0.04 | 0.48 | 0.02 | 22.7 | 37 | 36.9 | TR0_St19_5m_3p | Esp<U+00ED>rito Santo |
| X5n | Nano | Yes | 24696 | 6340 | 77360 | 5 | 0 | 21 | 5 | -26.23 | ... | 0.16 | 1.0900000000000001 | 0.15 | 0.9 | 0.05 | 22.8 | 98 | 36.9 | TR0_St21_5m_5n | Esp<U+00ED>rito Santo |
| X5p | Pico | Yes | 112590 | 16141 | 25341 | 5 | 0 | 21 | 5 | -26.23 | ... | 0.16 | 1.0900000000000001 | 0.15 | 0.9 | 0.05 | 22.8 | 98 | 36.9 | TR0_St21_5m_5p | Esp<U+00ED>rito Santo |
| X7n | Nano | Yes | 40829 | 8443 | 7667 | 7 | 0 | 26 | 5 | -27.31 | ... | 0.2 | 1.03 | 0.32 | 0.5 | 0.05 | 21.2 | 95.33 | 36.4 | TR0_St26_5m_7n | Esp<U+00ED>rito Santo |
| X7p | Pico | Yes | 22348 | 9254 | 26969 | 7 | 0 | 26 | 5 | -27.31 | ... | 0.2 | 1.03 | 0.32 | 0.5 | 0.05 | 21.2 | 95.33 | 36.4 | TR0_St26_5m_7p | Esp<U+00ED>rito Santo |
| X9n | Nano | Yes | 19193 | 8156 | 34 | 9 | 1 | 81 | 140 | -27.42 | ... | 0.2 | 1.64 | 0 | 0.26 | 7.0000000000000007E-2 | 17.3 | 553.79999999999995 | 35.9 | TR1_St81_140m_9n | Esp<U+00ED>rito Santo |
| X9p | Pico | Yes | 44610 | 29 | 53 | 9 | 1 | 81 | 140 | -27.42 | ... | 0.2 | 1.64 | 0 | 0.26 | 7.0000000000000007E-2 | 17.3 | 553.79999999999995 | 35.9 | TR1_St81_140m_9p | Esp<U+00ED>rito Santo |
| tri01n | Nano | Yes | 14162 | 11201 | 11792 | Trichod.1 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri01n | Esp<U+00ED>rito Santo |
| tri01p | Pico | Yes | 36576 | 14786 | 7772 | Trichod.1 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri01p | Esp<U+00ED>rito Santo |
| tri02n | Nano | Yes | 23906 | 14519 | 16934 | Trichod.2 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri02n | Sergipe |
| tri02p | Pico | Yes | 46889 | 15320 | 17259 | Trichod.2 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri02p | Sergipe |
| tri03n | Nano | Yes | 34892 | 24 | 21523 | Trichod.3 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri03n | Sergipe |
| tri03p | Pico | Yes | 55630 | 11558 | 15152 | Trichod.3 | 2 | Bloom | 0 | -27.80 | ... | NA | NA | NA | NA | NA | NA | NA | NA | TR2_StBloom_0m_tri03 | Sergipe |
phyloseq-class experiment-level object otu_table() OTU Table: [ 287 taxa and 55 samples ] sample_data() Sample Data: [ 55 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 287 taxa by 7 taxonomic ranks ]
In [ ]:
#Visualizar datos
sample_names(carbom)
rank_names(carbom)
sample_variables(carbom)
- 'X10n'
- 'X10p'
- 'X11n'
- 'X11p'
- 'X120n'
- 'X120p'
- 'X121n'
- 'X121p'
- 'X122n'
- 'X122p'
- 'X125n'
- 'X125p'
- 'X126n'
- 'X126p'
- 'X127n'
- 'X13n'
- 'X13p'
- 'X140n'
- 'X140p'
- 'X141n'
- 'X141p'
- 'X142n'
- 'X142p'
- 'X155n'
- 'X155p'
- 'X156n'
- 'X156p'
- 'X157n'
- 'X157p'
- 'X15n'
- 'X15p'
- 'X165n'
- 'X165p'
- 'X166n'
- 'X166p'
- 'X167n'
- 'X167p'
- 'X1n'
- 'X1p'
- 'X2n'
- 'X2p'
- 'X3n'
- 'X3p'
- 'X5n'
- 'X5p'
- 'X7n'
- 'X7p'
- 'X9n'
- 'X9p'
- 'tri01n'
- 'tri01p'
- 'tri02n'
- 'tri02p'
- 'tri03n'
- 'tri03p'
- 'Domain'
- 'Supergroup'
- 'Division'
- 'Class'
- 'Order'
- 'Family'
- 'Genus'
- 'fraction'
- 'Select_18S_nifH'
- 'total_18S'
- 'total_16S'
- 'total_nifH'
- 'sample_number'
- 'transect'
- 'station'
- 'depth'
- 'latitude'
- 'longitude'
- 'picoeuks'
- 'nanoeuks'
- 'bottom_depth'
- 'level'
- 'transect_distance'
- 'date'
- 'time'
- 'phosphates'
- 'silicates'
- 'ammonia'
- 'nitrates'
- 'nitrites'
- 'temperature'
- 'fluorescence'
- 'salinity'
- 'sample_label'
- 'costa'
In [ ]:
# vamos a conservar solo muestras para analizar (las que queremos analizar)
carbom <- subset_samples(carbom, Select_18S_nifH =="Yes")
carbom
phyloseq-class experiment-level object otu_table() OTU Table: [ 287 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 287 taxa by 7 taxonomic ranks ]
In [ ]:
# Mantenemos en este caso solo taxones fotosintéticos
carbom <- subset_taxa(carbom, Division %in% c("Chlorophyta", "Dinophyta", "Cryptophyta",
"Haptophyta", "Ochrophyta", "Cercozoa"))
carbom <- subset_taxa(carbom, !(Class %in% c("Syndiniales", "Sarcomonadea")))
carbom
phyloseq-class experiment-level object otu_table() OTU Table: [ 205 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 205 taxa by 7 taxonomic ranks ]
In [ ]:
# IMPORTANTE: Normalizar/escalar
# Normalizamos el número de lecturas en cada muestra utilizando la profundidad de secuenciación mediana.
# Normalizar en estadística se refiere a un proceso mediante el cual se ajustan los valores de una variable
# para que estén en una escala común y comparable con otras variables.
# En general, la normalización se utiliza para estandarizar los datos, de modo que las diferencias en la escala
# o el rango de valores entre las diferentes variables no afecten el resultado de los análisis estadísticos.
# Algunos ejemplos comunes son la normalización z-score, la normalización min-max y la normalización por percentil
total = median(sample_sums(carbom))
total
standf = function(x, t=total) round(t * (x / sum(x)))
standf
carbom = transform_sample_counts(carbom, standf)
carbom
44903
function (x, t = total)
round(t * (x/sum(x)))phyloseq-class experiment-level object otu_table() OTU Table: [ 205 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 205 taxa by 7 taxonomic ranks ]
In [ ]:
# El número de lecturas utilizadas para la normalización es 44903 .
plot_bar(carbom, fill = "Division")
carbom
phyloseq-class experiment-level object otu_table() OTU Table: [ 205 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 205 taxa by 7 taxonomic ranks ]
In [ ]:
# lo mismo pero más bonito
plot_bar(carbom, fill = "Division") +
geom_bar(aes(color=Division, fill=Division), stat="identity", position="stack")
In [ ]:
# ahora para la Clase
plot_bar(carbom, fill = "Class")
carbom
plot_bar(carbom, fill = "Class") +
geom_bar(aes(color=Class, fill=Class), stat="identity", position="stack")
phyloseq-class experiment-level object otu_table() OTU Table: [ 205 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 205 taxa by 7 taxonomic ranks ]
PREVALENCIA/ABUNDANCIA¶
Lo primero que podemos mirar es la prevalencia de las features taxonómicas.
Primero que podemos hacer es crear un data frame con los valores de prevalencia, luego les agregamos la taxonomía y graficamos.
Computamos prevalencia para cada feature y la guardamos en un data frame
la prevalencia se refiere a la proporción de individuos en una población que tienen una enfermedad o condición específica en un momento dado. Por lo tanto, una prevalencia del 5% indica que el 5% de la población estudiada tiene la enfermedad o condición en cuestión en el momento en que se llevó a cabo el estudio.
In [ ]:
prevcarbom = apply(X = otu_table(carbom),
MARGIN = ifelse(taxa_are_rows(carbom), yes = 1, no = 2),
FUN = function(x){sum(x > 0)})
# Le agregamos la taxonomía
prevcarbom = data.frame(Prevalence = prevcarbom,
TotalAbundance = taxa_sums(carbom),
tax_table(carbom))
plyr::ddply(prevcarbom, "Division", function(df1){cbind(mean(df1$Prevalence),sum(df1$Prevalence))}) -> dfprevcarbom
# podemos ver en la consola la prevalencia
prevcarbom
# Prevalence TotalAbundance Domain Supergroup Division Class
# Otu001 50 259644 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
# Otu002 54 359480 Eukaryota Hacrobia Haptophyta Prymnesiophyceae
# Otu003 52 279102 Eukaryota Archaeplastida Chlorophyta Mamiellophyceae
| Prevalence | TotalAbundance | Domain | Supergroup | Division | Class | Order | Family | Genus | |
|---|---|---|---|---|---|---|---|---|---|
| <int> | <dbl> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> | |
| Otu001 | 50 | 259644 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu002 | 54 | 359480 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | UCYN_A1_host |
| Otu003 | 52 | 279102 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu004 | 50 | 151580 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Prorocentrum |
| Otu005 | 28 | 45560 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Mediophyceae | Mediophyceae_X | Thalassiosira |
| Otu006 | 22 | 47960 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Pseudo_nitzschia |
| Otu007 | 42 | 84868 | Eukaryota | Stramenopiles | Ochrophyta | Pelagophyceae | Pelagophyceae_X | Pelagophyceae_X | Pelagomonas |
| Otu008 | 34 | 59937 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu009 | 43 | 92316 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiales | Chrysochromulinaceae | Chrysochromulina |
| Otu011 | 29 | 53322 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_C | Chrysophyceae_Clade_C_X |
| Otu012 | 18 | 48556 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Gonyaulax |
| Otu014 | 41 | 54301 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_G | Chrysophyceae_Clade_G_X |
| Otu015 | 32 | 52928 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu018 | 40 | 56796 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Pedinellales | Pedinellales_X |
| Otu020 | 20 | 39708 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | Braarudosphaera |
| Otu021 | 19 | 14861 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu022 | 33 | 37498 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Prymnesiophyceae_X | Syracosphaera |
| Otu023 | 32 | 32811 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Bacillariophyceae_X |
| Otu025 | 22 | 35716 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu026 | 19 | 32017 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Cylindrotheca |
| Otu027 | 21 | 23263 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Suessiales | Suessiales_X | Karlodinium |
| Otu028 | 38 | 33453 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Isochrysidales | Noelaerhabdaceae | Emiliania |
| Otu030 | 22 | 24661 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
| Otu032 | 24 | 15784 | Eukaryota | Archaeplastida | Chlorophyta | Prasino_Clade_VII | Prasino_Clade_VII_X | Prasino_Clade_VII_A | Prasino_Clade_VII_A_4_X |
| Otu033 | 10 | 19643 | Eukaryota | Archaeplastida | Chlorophyta | Ulvophyceae | Ulvales_relatives | Ulvales_relatives_X | Ulva |
| Otu034 | 13 | 32984 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu035 | 29 | 36098 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_G | Chrysophyceae_Clade_G_X |
| Otu036 | 8 | 6566 | Eukaryota | Hacrobia | Haptophyta | Haptophyta_HAP2 | Haptophyta_HAP2 | Haptophyta_HAP2 | Haptophyta_HAP2_X |
| Otu037 | 11 | 9060 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Pseudo_nitzschia |
| Otu038 | 23 | 23969 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_G | Chrysophyceae_Clade_G_X |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| Otu241 | 3 | 22 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Mediophyceae | Mediophyceae_X | Mediophyceae_X |
| Otu242 | 12 | 26 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu245 | 4 | 12 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu247 | 1 | 15 | Eukaryota | Stramenopiles | Ochrophyta | Pelagophyceae | Pelagophyceae_X | Pelagophyceae_X | Aureococcus |
| Otu248 | 1 | 9 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophytceae | Bacillariaceae | Fragilariopsis |
| Otu249 | 2 | 24 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu250 | 2 | 21 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Dictyochales | Dictyochales_X |
| Otu251 | 10 | 17 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu252 | 2 | 20 | Eukaryota | Archaeplastida | Chlorophyta | Chlorophyceae | NA | NA | Chlorophyceae_X |
| Otu253 | 1 | 14 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu254 | 12 | 19 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu255 | 1 | 10 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyta_X | Bacillariophyta_X | Bacillariophyta_X |
| Otu257 | 5 | 28 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Pedinellales | Pedinellales_X |
| Otu259 | 3 | 21 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
| Otu260 | 2 | 9 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyta_X | Bacillariophyta_X | Bacillariophyta_X |
| Otu263 | 1 | 9 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu268 | 8 | 14 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu272 | 3 | 36 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu273 | 2 | 40 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Mamiellaceae | Micromonas |
| Otu274 | 2 | 13 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Prymnesiophyceae_X | Braarudosphaeraceae | UCYN_A1_host |
| Otu276 | 1 | 10 | Eukaryota | Stramenopiles | Ochrophyta | Dictyochophyceae | Dictyochophyceae_X | Pedinellales | Pedinellales_X |
| Otu277 | 2 | 16 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu279 | 2 | 13 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Calcihaptophycidae | Rhabdosphaeraceae | Algirosphaera |
| Otu280 | 2 | 4 | Eukaryota | Stramenopiles | Ochrophyta | Bacillariophyta | Bacillariophyceae | Bacillariophyceae_X | Pseudo_nitzschia |
| Otu281 | 1 | 7 | Eukaryota | Stramenopiles | Ochrophyta | Chrysophyceae | Chrysophyceae_X | Chrysophyceae_Clade_C | Chrysophyceae_Clade_C_X |
| Otu282 | 2 | 7 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Ostreococcus |
| Otu283 | 6 | 9 | Eukaryota | Archaeplastida | Chlorophyta | Mamiellophyceae | Mamiellales | Bathycoccaceae | Bathycoccus |
| Otu285 | 2 | 23 | Eukaryota | Alveolata | Dinophyta | Dinophyceae | Dinophyceae_X | Dinophyceae_X | Dinophyceae_X |
| Otu286 | 1 | 4 | Eukaryota | Hacrobia | Haptophyta | Prymnesiophyceae | Isochrysidales | Noelaerhabdaceae | Emiliania |
| Otu287 | 3 | 11 | Eukaryota | Hacrobia | Cryptophyta | Cryptophyceae | Cryptophyceae_X | Cryptomonadales | Teleaulax |
In [ ]:
# Otra forma de verlo (División) es de forma gráfica, asi:
prevcarbom1 = subset(prevcarbom, Division %in% get_taxa_unique(carbom, "Division"))
ggplot(prevcarbom1, aes(TotalAbundance, Prevalence / nsamples(carbom),color=Division)) +
# Agregamos una línea para nuestro umbral
geom_hline(yintercept = 0.05, alpha = 0.5, linetype = 2) + geom_point(size = 2, alpha = 0.7) +
scale_x_log10() + xlab("Total Abundance") + ylab("Prevalence [Frac. Samples]") +
facet_wrap(~Division) + theme(legend.position="none")
In [ ]:
# en este caso la variamos con el Supergroup
prevcarbom2 = subset(prevcarbom, Supergroup %in% get_taxa_unique(carbom, "Supergroup"))
ggplot(prevcarbom2, aes(TotalAbundance, Prevalence / nsamples(carbom),color=Supergroup)) +
# Agregamos una línea para nuestro umbral
geom_hline(yintercept = 0.25, alpha = 0.5, linetype = 2) + geom_point(size = 2, alpha = 0.7) +
scale_x_log10() + xlab("Total Abundance") + ylab("Prevalence [Frac. Samples]") +
facet_wrap(~Supergroup) + theme(legend.position="none")
In [ ]:
# Definimos el umbral de prevalencia a un 5%
(prevalenceThreshold = 0.05 * nsamples(carbom))
# [1] 2.7
keepTaxa = rownames(prevcarbom2)[(prevcarbom2$Prevalence >= prevalenceThreshold)]
(carbom2 = prune_taxa(keepTaxa, carbom))
2.7
phyloseq-class experiment-level object otu_table() OTU Table: [ 143 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 143 taxa by 7 taxonomic ranks ]
Y asi podriamos hacerlo con los datos que quisieramos. Si os fijais en el excel existe una columna llamada "fraction" con dos valores: Pico y Nano en el estudio, hace referencia a la composición de pico y nano-fitoplancton en el area Atlántico Sur frente a Brasil este analisis de clasificación se llevo a cabo por citometría de flujo
In [ ]:
# nosotros podemos realizar un analisis de composición de pico vs nano-fitoplancton, entonces reagrupamos muestras Pico vs Nano
carbom_fraction <- merge_samples(carbom, "fraction")
plot_bar(carbom_fraction, fill = "Division") +
geom_bar(aes(color=Division, fill=Division), stat="identity", position="stack")
# y vemos la abundancia de nano vs pico
Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on" Warning message in asMethod(object): "NAs introducidos por coerci'on"
In [ ]:
# podemos tambien hacer paneles separados Pico vs Nano y Surface vs muestras Deep
carbom_chloro <- subset_taxa(carbom, Division %in% c("Chlorophyta"))
plot_bar(carbom_chloro, x="Division", fill = "Division", facet_grid = level~fraction) +
geom_bar(aes(color=Genus, fill=Genus), stat="identity", position="stack")
In [ ]:
# Division
carbom_chloro <- subset_taxa(carbom, Division %in% c("Chlorophyta"))
plot_bar(carbom_chloro, x="Genus", fill = "Genus", facet_grid = level~fraction) +
geom_bar(aes(color=Genus, fill=Genus), stat="identity", position="stack")
In [ ]:
set.seed(4235421)
# proj <- get_ordination(pseq, "MDS", "bray")
ord <- ordinate(carbom, "MDS", "bray")
In [ ]:
plot_ordination(carbom, ord, color = "fraction") +
geom_point(size = 5)
MAPAS DE CALOR/HEATMAP¶
NMDS son las siglas en inglés de Nonmetric Multidimensional Scaling, lo que en español se traduce como "Escalamiento Multidimensional No Métrico". Es una técnica estadística utilizada para visualizar y analizar datos de similitud o disimilitud entre objetos o individuos en el contexto de la metagenómica, se enfoca en el estudio del material genético presente en comunidades microbianas complejas.
In [ ]:
# en este caso el análisis NMDS de comunidades se baso en las principales OTU de ARNr 18S se realizó utilizando la distancia de Bray-Curtis
plot_heatmap(carbom, method = "NMDS", distance = "bray")
Warning message: "Transformation introduced infinite values in discrete y-axis"
Está muy muy desordenado. Es mejor considerar solo las OTU más abundantes para los mapas de calor. Por ejemplo, solo se pueden tomar OTU que representen al menos el 20 % de las lecturas en al menos una muestra. Recordemos que normalizamos todas las muestras a la mediana del número de lecturas (total). Nos quedamos entonces solo con 33 OTUS lo que facilita mucho la lectura.
In [ ]:
carbom_abund <- filter_taxa(carbom, function(x) sum(x > total*0.20) > 0, TRUE)
carbom_abund
otu_table(carbom_abund)[1:8, 1:5]
plot_heatmap(carbom_abund, method = "NMDS", distance = "bray")
phyloseq-class experiment-level object otu_table() OTU Table: [ 33 taxa and 54 samples ] sample_data() Sample Data: [ 54 samples by 28 sample variables ] tax_table() Taxonomy Table: [ 33 taxa by 7 taxonomic ranks ]
| X10n | X10p | X11p | X120n | X120p | |
|---|---|---|---|---|---|
| Otu001 | 13339 | 7346 | 3804 | 12662 | 3 |
| Otu002 | 18 | 8329 | 14958 | 30 | 36206 |
| Otu003 | 9692 | 10488 | 20 | 16537 | 11 |
| Otu004 | 3584 | 4943 | 33 | 7 | 9 |
| Otu005 | 0 | 6 | 11 | 0 | 5 |
| Otu006 | 0 | 9 | 0 | 0 | 5 |
| Otu007 | 4473 | 605 | 587 | 5894 | 3 |
| Otu008 | 1 | 9 | 6707 | 2 | 17 |
Warning message: "Transformation introduced infinite values in discrete y-axis"
In [ ]:
# otro ejemplo seria con esta metodologia: CCA/euclidean
plot_heatmap(carbom_chloro, method = "CCA", distance = "euclidean",
taxa.label = "Genus", taxa.order = "Genus",
low="beige", high="black", na.value="beige")
Warning message: "Transformation introduced infinite values in discrete y-axis"
In [ ]:
# Tambien es posible utilizar diferentes distancias y diferentes métodos multivariantes.
# Por ejemplo, distancia Jaccard y MDS y etiquetar OTU con Clase, ordenar por Clase.
# También podemos cambiar la Paleta (la paleta por defecto es un poco fea…).
plot_heatmap(carbom_abund, method = "MDS", distance = "(A+B-2*J)/(A+B-J)",
taxa.label = "Class", taxa.order = "Class",
trans=NULL, low="beige", high="red", na.value="#04162c")
# tenemos opciones de utilizar muchas distancias integradas diferentes
dist_methods <- unlist(distanceMethodList)
print(dist_methods)
UniFrac1 UniFrac2 DPCoA JSD vegdist1 vegdist2
"unifrac" "wunifrac" "dpcoa" "jsd" "manhattan" "euclidean"
vegdist3 vegdist4 vegdist5 vegdist6 vegdist7 vegdist8
"canberra" "bray" "kulczynski" "jaccard" "gower" "altGower"
vegdist9 vegdist10 vegdist11 vegdist12 vegdist13 vegdist14
"morisita" "horn" "mountford" "raup" "binomial" "chao"
vegdist15 betadiver1 betadiver2 betadiver3 betadiver4 betadiver5
"cao" "w" "-1" "c" "wb" "r"
betadiver6 betadiver7 betadiver8 betadiver9 betadiver10 betadiver11
"I" "e" "t" "me" "j" "sor"
betadiver12 betadiver13 betadiver14 betadiver15 betadiver16 betadiver17
"m" "-2" "co" "cc" "g" "-3"
betadiver18 betadiver19 betadiver20 betadiver21 betadiver22 betadiver23
"l" "19" "hk" "rlb" "sim" "gl"
betadiver24 dist1 dist2 dist3 designdist
"z" "maximum" "binary" "minkowski" "ANY"
También podemos construir nuestras propias distancias.
Para los vectores x e y, los términos "cuadráticos" son J = sum(x*y), A = sum(x^2), B = sum(y^2) y los términos "mínimos" son J = sum(pmin(x ,y)), A = sum(x) y B = sum(y), y los términos "binarios" son cualquiera de estos después de transformar los datos en forma binaria (número compartido de especies y número de especies para cada fila).
Algunos ejemplos:
A+B-2*J “cuadrático” euclidiano al cuadrado
A+B-2*J “mínimo” Manhattan
(A+B-2*J)/(A+B) “mínimo” Bray-Curtis
(A+B-2*J)/(A+B) “binario” Sørensen
A+B-2*J)/(A+BJ) Jaccard “binario”
Otra estrategia es hacer un mapa de calor para un grupo de taxonomía específico.
In [ ]:
# Por ejemplo, podemos apuntar a Chlorophyta y luego etiquetar las OTU usando el Género.
plot_heatmap(carbom_chloro, method = "NMDS", distance = "bray",
taxa.label = "Genus", taxa.order = "Genus",
low="beige", high="red", na.value="beige")
Warning message: "Transformation introduced infinite values in discrete y-axis"
Medidas de riqueza/rarefacción, uniformidad, dominancia, diversidad filogenética (diversidad alfa)¶
La rarefacción es un método utilizado en ecología para estandarizar la comparación de la diversidad de muestras con diferentes tamaños. Consiste en seleccionar una submuestra aleatoria del mismo tamaño (basado en la muestra más pequeña) de cada muestra y comparar los resultados. De esta manera, se estandariza la comparación y se evita que la diversidad de una muestra se vea afectada por el tamaño de la muestra.
DIVERSIDAD ALFA¶
Las medidas de diversidad alfa se utilizan para identificar la riqueza y uniformidad dentro de los taxones individuales. Las métricas/índices comúnmente utilizados son Shannon, Inverse Simpson, Simpson, Gini, Observed y Chao1. Estos índices no tienen en cuenta la filogenia de los taxones identificados en la secuenciación. La diversidad filogenética (PD de Faith) utiliza la distancia filogenética para calcular la diversidad de una muestra determinada.
Observad (simplemente el número de taxa o riqueza),
Chao1 (la riqueza ajustada por probabilidad de no observar especies),
ACE (riqueza que toma en cuenta la abundancia relativa),
Shannon (abundancia relativa de taxa),
Simpson (1 - la probabilidad de que observemos aleatoriamente dos bacterias en una comunidad y que pertenezcan a diferentes especies ),
Inverse Simpson ( 1 / Simpson),
Fisher (riqueza tomando en cuenta abundancia).
Es importante señalar que los índices de diversidad alfa son sensibles al ruido inherente a la aplicación de la reacción en cadena de la polimerasa y los errores de secuenciación.
Uno tiene que considerar la profundidad de secuenciación (cuántos taxones han sido muestreados) para cada muestra. Si hay una gran diferencia, entonces es importante normalizar las muestras a la misma profundidad de muestreo. Primero, observamos la profundidad de muestreo (cantidad de lecturas por muestra).
In [ ]:
# En phyloseq simplemente llamamos la función plot_richness y podemos visualizar las medidas de diversidad
# CON LOS ESTIMADORES OBSERVED, SHANON Y CHAO1
# aca lo hacemos con fraction (Pico-Nano) vs level (Sur-Deep)
plot_richness(carbom, color = "fraction", x= "level", measures = c("Observed", "Chao1", "Shannon")) + geom_boxplot(aes(fill = fraction), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
Las muestras Pico suelen ser menos diversas que las Nano cuando se observa la riqueza (Observed y Chao1), pero esta tendencia se invierte cuando se considera el índice de Shannon en el nivel.
Los puntos individuales fuera de las cajas representan outliers o valores atípicos, que son muestras con valores de diversidad mucho más altos o bajos que el resto en su grupo.
In [ ]:
# otro ejemplo
plot_richness(carbom, color = "Select_18S_nifH", x= "level", measures = c("Observed", "Chao1", "Shannon")) + geom_boxplot(aes(fill = Select_18S_nifH), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
plot_richness(carbom, color = "Select_18S_nifH", x= "level", measures = c("ACE", "Chao1", "Fisher")) + geom_boxplot(aes(fill = Select_18S_nifH), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
In [ ]:
# Trazar estimador de riqueza Chao1 y estimador de diversidad de Shannon para todo carbom (otus)
plot_richness(carbom, measures=c("Chao1", "Shannon"))
In [ ]:
# Reagrupar muestras de la misma fracción.
plot_richness(carbom, measures=c("Chao1", "Shannon"), x="level", color="fraction")
DIVERSIDAD ENTRE ESPECIES BETA¶
En este ejercicio nos interesa comparar la diversidad entre divsiones
Recordemos que varias divisiones de organismos (ver tabla).
Necesitamos crear una lista de comparasiones de a pares para poder visualizar y calcular significancia estadística de manera simultánea.
En cuanto a diversidad beta podemos calcular similitud global a través de todas las muestras de interés o también podemos cuantificar la divergencia de un grupo y compararla con la divergencia de otro.
In [ ]:
# Veamos este caso primero.
# Calculamos las divergencias para la division Chlorophyta (subgrupo: Archaeplastida) y Dinophyta (subgrupo: Alveolata)
div.Archaeplastida <- divergence(subset_taxa(carbom, Division == "Chlorophyta"), apply(abundances(subset_taxa(carbom, Division == "Chlorophyta")), 1, median))
div.Alveolata <- divergence(subset_taxa(carbom, Division == "Dinophyta"), apply(abundances(subset_taxa(carbom, Division == "Dinophyta")), 1, median))
# transformamos el resultado anterior en _dataframes_
data.frame(div.Archaeplastida) -> df.div.Archaeplastida
data.frame(div.Alveolata) -> df.div.Alveolata
# Gather
df.div.Archaeplastida <- gather(df.div.Archaeplastida, taxa, divergence)
df.div.Alveolata <- gather(df.div.Alveolata, taxa, divergence)
# Agregamos columnas a nuestros _dataframes_
conflicts_prefer(ggpubr::mutate) # solución a problemas de conflicto
conflicts_prefer(ggpubr::mutate) # solución a problemas de conflicto
mutate(df.div.Archaeplastida, Division = "Archaeplastida") -> df.div.Archaeplastida
mutate(df.div.Alveolata, Division = "Alveolata") -> df.div.Alveolata
# Cambiamos los nombres de las columans de manera que sean iguales an ambos _dataframes_
colnames(df.div.Archaeplastida) <- c("taxa", "divergence", "Division")
colnames(df.div.Alveolata) <- c("taxa", "divergence", "Division")
# Los combinamos en un _dataframe_
rbind(df.div.Archaeplastida, df.div.Alveolata) -> div.boxplot
# Y finalmente graficamos y realizamos una comparación estadística
p2 <- ggboxplot(data = div.boxplot, x = "Division", y = "divergence", fill = "Division", palette = c("#a6cee3", "#fdbf6f"))
p2 + stat_compare_means(comparisons = list(c("Archaeplastida", "Alveolata")))
[conflicted] Removing existing preference. [conflicted] Will prefer ggpubr::mutate over any other package. [conflicted] Removing existing preference. [conflicted] Will prefer ggpubr::mutate over any other package.
Divergencia: La "divergencia" se refiere, en este contexto, a la variabilidad genética o diferencia en las secuencias de ADN/ARN de los organismos pertenecientes a las dos divisiones.
Comparación entre Divisiones:
Archaeplastida: Esta división tiene una mediana de divergencia más alta en comparación con Alveolata. También tiene varios valores atípicos en el rango inferior. Alveolata: Esta división tiene una mediana de divergencia ligeramente más baja y también presenta valores atípicos, pero en el rango superior. La cifra 0.023 entre las dos cajas sugiere que hay una diferencia estadísticamente significativa entre las medianas de las dos divisiones con un valor de p de 0.023. Esto significa que es probable que la diferencia observada entre las dos divisiones no se deba al azar.
Existen diferentes medidas de similitud (o disimilitud) disponibles que nos permiten entender las relaciones entre nuestras muestras.
En general todas producen matrices de distancia comparables.
El paquete phyloseq ofrece un gran número de medidas de distancia.
Las más populares son UniFrac y Weighted UniFrac (medidas que consideran filogenia) y otras independientes de filogenia como: Jaccard, Manhattan, Euclidian, Bray-Curtis, Canberra, etc.
In [ ]:
# ej independiente de filogenia.
# los datos de "costa" han sido inventados"
carbom.mds.bray <- ordinate(carbom, method = "MDS", distance = "bray")
evals <- carbom.mds.bray$values$Eigenvalues
pord1 <- plot_ordination(carbom, carbom.mds.bray, color = "costa") +
labs(col = "costa") +
coord_fixed(sqrt(evals[2] / evals[1]))
grid.arrange(pord1)
ORDENACIÓN¶
In [ ]:
# análisis multivariable basado en la distancia de Bray-Curtis y la ordenación NMDS
carbom.ord <- ordinate(carbom, "NMDS", "bray")
# Trazamos OTU
plot_ordination(carbom, carbom.ord, type="taxa", color="Class", shape= "Division",
title="OTUs")
Square root transformation Wisconsin double standardization Run 0 stress 0.2317058 Run 1 stress 0.244209 Run 2 stress 0.2451212 Run 3 stress 0.2626792 Run 4 stress 0.2624512 Run 5 stress 0.259957 Run 6 stress 0.2503071 Run 7 stress 0.2556401 Run 8 stress 0.2488113 Run 9 stress 0.2581377 Run 10 stress 0.2302727 ... New best solution ... Procrustes: rmse 0.106655 max resid 0.3795624 Run 11 stress 0.2650893 Run 12 stress 0.2626179 Run 13 stress 0.2456273 Run 14 stress 0.2502234 Run 15 stress 0.2510932 Run 16 stress 0.2492831
Run 17 stress 0.26479
Run 18 stress 0.2506902
Run 19 stress 0.2519276
Run 20 stress 0.2487789
*** Best solution was not repeated -- monoMDS stopping criteria:
20: stress ratio > sratmax
Un poco confuso, así que hacemos que sea más fácil de visualizar dividiéndolo según la división taxonómica.
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plot_ordination(carbom, carbom.ord, type="taxa", color="Class",
title="OTUs", label="Class") +
facet_wrap(~Division, 3)
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# Ahora mostramos ejemplos y amplíamos los puntos para que sea más fácil de leer.
plot_ordination(carbom, carbom.ord, type="samples", color="fraction",
shape="level", title="Samples") + geom_point(size=3)
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# ahora vemos muestras y OTU pero en 2 paneles diferentes.
plot_ordination(carbom, carbom.ord, type="split", color="Class",
shape="level", title="biplot", label = "station") +
geom_point(size=3)
ANALISIS DE REDES¶
Para finalizar, vamos a echar un vistazo a las capacidades de phyloseq para generar redes de co-occurrencia.
Las redes de co-ocurrencia nos dan pistas sobre potenciales interacciones ecológicas entre organismos.
Estas interacciones pueden ser directas o indirectas (no lo podemos determinar a partir de una red) y nos permiten comenzar a descifrar mecanismos ecológicos detrás de la composición de una comunidad microbiana.
En general en ecología tenemos distintos tipos de interacciones:
mutalismo, comensalismo, predación, amensalismo, competición o mutua depredación
Donde destacan depredación, competición o depredación mutua, y mutualismo.
Cada una de estas relaciones podría ser detectada en una red de co-ocurrencia según patrones de correlación positivos o negativos.
Veamos como generaríamos una red en phyloseq
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# Análisis de red simple
plot_net(carbom, distance = "(A+B-2*J)/(A+B)", type = "taxa",
maxdist = 0.8, color="Class", point_label="Genus")
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# Esto es bastante confuso. Hagámoslo más simple usando solo OTU principales
plot_net(carbom, distance = "(A+B-2*J)/(A+B)", type = "taxa",
maxdist = 0.9, color="Class", point_label="Genus")
plot_net(carbom, type = "taxa", point_label = "Genus",
point_size = 10, point_alpha = 0.5, maxdist = 0.5, distance = "(A+B-2*J)/(A+B)", color= "Class", laymeth = "auto")
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# parecido
plot_net(carbom, type = "taxa", point_label = "Genus", point_size = 10, point_alpha = 0.5, maxdist = 0.5, color = "Class", distance = "(A+B-2*J)/(A+B)", laymeth = "auto")
IMPORTANTE!¶
La red generada con phyloseq no es una red de co-ocurrencia propiamente, es más bien una red que representa relaciones de distancia entre taxa o muestras. En nuestro ejemplo usamos muestras. Para una red de co-ocurrencia propiamente tal necesitamos usar las funciones del paquete: SpiecEasi
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library(SpiecEasi)
se.mb.psd4 <- spiec.easi(carbom, method = 'mb', lambda.min.ratio=1e-2,
nlambda=20, icov.select.params = list(rep.num=50))
# Obtener la matriz de adyacencia y convertirla a una matriz densa
adj_matrix <- getRefit(se.mb.psd4)
dense_adj_matrix <- as.matrix(adj_matrix)
# Crear el grafo usando la matriz densa
ig2.mb <- igraph::graph.adjacency(dense_adj_matrix, mode="undirected", weighted=TRUE, diag=FALSE)
V(ig2.mb)$name <- taxa_names(carbom)
plot_network(ig2.mb, carbom, type = "taxa", color = "Genus")
Applying data transformations... Selecting model with pulsar using stars... Fitting final estimate with mb... done
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se.glasso <- spiec.easi(carbom, method = 'mb', lambda.min.ratio=1e-2,
nlambda=20, icov.select.params = list(rep.num=50))
# Obtener la matriz de adyacencia y convertirla a una matriz densa
adj_matrix <- getRefit(se.mb.psd4)
dense_adj_matrix <- as.matrix(adj_matrix)
# Crear el grafo usando la matriz densa
ig2.mb <- igraph::graph.adjacency(dense_adj_matrix, mode="undirected", weighted=TRUE, diag=FALSE)
V(ig2.mb)$name <- taxa_names(carbom)
plot_network(ig2.mb, carbom, type = "taxa", color = "Supergroup")
Applying data transformations... Selecting model with pulsar using stars...
Fitting final estimate with mb... done
Si se ven pocas conexiones en el gráfico, podría deberse a varias razones:
Interacciones Fuertes: spiec.easi busca interacciones fuertes y significativas en los datos. Si hay pocas conexiones, podría ser una indicación de que solo se han identificado pocas interacciones fuertes y confiables en tu conjunto de datos.
Parámetros del Modelo: La elección de parámetros para spiec.easi puede influir en el número de aristas identificadas. Por ejemplo, lambda.min.ratio y nlambda pueden ajustarse para identificar más o menos interacciones. Puede intentar ajustar estos parámetros para ver si obtiene más conexiones.